The Cameroon international capped a fine performance down the left flank with a delightful strike for the three points.
That goal came after 51 minutes of a pulsating encounter. Jamie Redknapp led a break, carrying the ball for 30 yards before releasing Atouba who moved towards the back-tracking Stephen Carr, switched the ball to his right foot and curled across Shay Given into the far corner from 20 yards.
Jacques Santini's first Premiership win was no less than we deserved after hanging in there under pressure in the first half before having the better of it for the first 20 minutes of the second half.
Naturally, the home side came back for a late burst - no surprise with Bellamy, Shearer, Kluivert, Ameobi and Dyer all on - but they carved out only one decent chance in the last 10 minutes, wasted by Ameobi.
Ledley King was outstanding and led a gutsy defensive display that saw Paul Robinson called into serious action only twice. His first save, tipping over James Milner's sweet volley, was right out of the top drawer.
The midfield worked their socks off, not least in the opening and closing spells while Fredi Kanoute and Jermain Defoe were always a handful, Defoe causing Andy O'Brien and Andy Hughes all sorts of problems.
Apart from Milner's volley, Newcastle's best chances of the first half fell to the impressive Jermaine Jenas who poked just wide after latching onto Robert's cross before watching his towering header from Robert's corner hit Bellamy on the back.
At the other end, Defoe didn't quite get hold of a shot after typically working a yard of space - something he did all afternoon - and Atouba gave no indication of what would follow after the break by crashing two or three half-chances into the Gallowgate End!
That all changed six minutes into the second half and our best move followed soon after as Sean Davis flicked a ball around the corner for Defoe who controlled and shot only for Given to block with his legs.
Typically of the game, Newcastle hit back straight away as Shearer laid the ball back for Robert to strike but Robinson was equal to the task.
We had two chances in two minutes to kill the game off as King's header was cleared off the line by Carr and Michael Brown failed to connect with Defoe's cross but Bobby Robson went for broke with 15 minutes left - on came Kluivert, Dyer and Ameobi in a triple substitution - and the rest of the game was played in our third of the field.
However, the home side's possession only led to one chance as Ameobi failed to connect with Bernard's cross.
MINUTE BY MINUTE GUIDE
1min: Carr's ball over the top for Shearer but Robinson out quickly to gather.
2mins: Bellamy onto Robert's pass, into box, left-foot shot looked like it was going wide but Robinson fine save anyway.
2mins: Confusion from corner, Robinson dived to punch away danger.
4mins: Shearer struck free-kick, 20 yards, straight into wall.
7mins: CHANCE. Kanoute good hold up play and skipped away from Bernard, low cross controlled by Defoe, worked a yard on O'Brien but didn't connect properly with left foot from 10 yards, straight at Given.
10mins: Decent spell now, Redknapp 25-yarder moved in air but straight at Given.
11mins: CHANCE. Jenas onto Robert pass as Naybet slipped, clean run to goal, left side, Robinson out to narrow angle and Jenas poked ball just wide.
13mins: Bellamy away from three challenges along byline, attempted cross cut out.
17mins: Naybet crucial interception as Bellamy looked to play in Jenas.
18mins: Great diving defensive header from King to clear Bellamy's dangerous cross.
21mins: Davis initially played in Kanoute, might have shot but held up and crossed deep, ball fell at feet of Atouba who snatched right foot shot into Gallowgate End.
24mins: More good possession, Redknapp driven cross from right ended up with Davis on edge of box, helped on to Atouba, this time acrobatic shot over.
26mins: SAVE. Deep cross from Carr headed back to Milner by Shearer, Milner couldn't have caught volley better from 16 yards, Robinson alive to tip over.
28mins: Good leap and header from Atouba to Redknapp's deep free-kick, Kanoute onto second ball but could only loop header to Given.
30mins: Jenas won crunching 50-50 with Edman, Bellamy onto loose ball, pull back destined for Jenas but Ifil across to cover.
32mins: CLOSE. Jenas towering header from Robert's corner but goal bound effort hit Bellamy. Ifil and Mendes also waiting on the line.
35mins: Strong run by Defoe, away from O'Brien, played square to Kanoute, shot blocked by Hughes.
37mins: Shearer did well to overhead kick deep Robert cross back into play, ball eventually met on volley by Jenas but flew wide.
39mins: Superb defending by Naybet, kept breaking Bellamy down left channel and when he switched inside, blocked shot.
44mins: Mendes released Kanoute, pinpoint cross volleyed high and wide by Atouba.
Half-time: Newcastle United 0, Spurs 0
50mins: Defoe almost made something out of Robinson's long kick, crowded out, stabbed shot wide.
51mins: GOAL. Redknapp led break, carried ball for 30 yards, played it wide to Atouba who ran at Carr, switched to his right foot and curled into corner from 20 yards. 1-0.
57mins: Another brilliant defensive header from King as he and Shearer dived in for Robert's cross.
59mins: CLOSE. Robert free-kick from right side of box looked on target until deflected over the bar.
62mins: CHANCE. Our move of game, Atouba into feet of Davis who flicked ball around the corner to Defoe into the box, left foot shot blocked by Given's feet.
63mins: SAVE. Bernard into Shearer, held up ball before laying back to Robert, shot tipped around post by Robinson.
68mins: YELLOWS. Redknapp and Robert for minor skirmish, although Robert smashed ball at Redknapp at the end of it.
69mins: SUB. Brown for Redknapp.
70mins: Defoe again made something out of nothing, onto Atouba flick, quick spin and shot low to near post, safely gathered by Given.
72mins: OFF LINE. Brown's corner, Atouba near post flick, diving header from King cleared off the line by Carr.
73mins: Robert low skidder tricky for Robinson but behind it all the way.
74mins: CHANCE. Defoe lightning fast to byline, pulled all over the place but cut back for Brown who failed to connect under pressure six yards out.
75mins: SUBS. Dyer, Kluivert and Ameobi for Robert, Milner and Jenas.
80mins: SUB. Gardner for Kanoute.
84mins: Davis break forward, laid to Defoe, skipped wide of Hughe sbut slight hesitation allowed defender back to block shot.
87mins: CHANCE. Plenty of Newcastle pressure now - low cross from left by Bernard found its way to Ameobi who made complete hash of finish 12 yards out.
89mins: SUB. Jackson for Atouba.
89mins: YELLOW. Brown for foul on Bellamy.
Line-ups: Newcastle United: Given, Carr, O'Brien, Hughes, Barnard, Butt, Jenas (Dyer, 74), Milner (Ameobi, 74), Robert (Kluivert, 74), Shearer, Bellamy. Unused subs: Harper, Elliott.
Spurs: Robinson, Ifil, Naybet, King, Edman, Redknapp (Brown, 69), Davis, Mendes, Atouba (Jackson, 89), Defoe, Kanoute (Gardner, 80). Subs: Keller, Silva.
Referee: Mike Dean.
Thimothee Atouba completed a dream full debut as we recorded only our second win at St James Park in 10 years on Saturday.