The Mali hitman picked up a fine reverse pass from Michael Brown, shifted the ball past Richard Dunne and lashed into David James' top right corner from 16 yards in the 56th minute for our first win at the City of Manchester Stadium.
It was no less then we deserved after creating the better chances in the first half and it could have been three or four more but for wasteful finishing following Kanoute's strike.
Those misses mattered little in the end though as we recorded a third-successive win and the fourth on our travels this season.
Rohan Ricketts, Noe Pamarot and Kanoute came back into the starting line-up with Robbie Keane overcoming a late injury scare.
Neither side produced fluent football in the first half but there were few doubts that we created the better chances.
The first was made and missed by Ricketts after 25 minutes, picking up the ball on the left, cutting into the box, jinking past Danny Mills and Dunne only to slide the ball agonisingly wide.
The second fell to Keane after Pedro Mendes spotted his run and delivered the perfect pass, Keane sprinted clear of City's back line and through on James only to lob just wide.
At the other end, Paul Robinson was forced into serious action just once when the ever-competitive Joey Barton hit a dipper from 25 yards that the keeper did well to tip wide. Later in the half, Antoine Sibierski strained to reach Jordan's cross but couldn't keep his header on target.
Otherwise it was fairly scrappy, stop-start stuff with City enjoying the better of possession but always running into Noureddine Naybet and Ledley King.
Martin Jol made changes at the interval with Stephen Kelly and Anthony Gardner on for Mendes and Naybet.
City were never really at the races in the second half. They only had one serious attempt when Robbie Fowler's struck low through a crowd of bodies and Robinson held on well with Jon Macken hovering. That was after 64 minutes and the last thing Robinson had to do.
Kanoute's super striker arrived 11 minutes into the half and, once again, we were guilty of not killing the opposition off.
Keane saw Silvain Distin clear his shot off the line from a narrow angle and was left holding his head after somehow shooting over from five yards from Brown's low cross.
Brown was excellent and clearly relished this return to his former club, Naybet and King and then Gardner were unmoved, Ricketts showed flashes from wide right, Keane buzzed around and Kanoute took his goal superbly. All in all, the right result.
GUIDE TO THE ACTION
1min: Fowler turned away from Naybet, early pass into Macken, King too strong for the striker who went down, certainly no penalty.
3mins: Wright-Phillips hooked ball onto roof of net, attempted cross, no danger.
7mins: Our first attack, Kanoute back heel to Ricketts, Brown late run to meet cross but handled it.
14mins: SAVE. Wright-Phillips cross half-cleared to Barton 25 yards out, control and dipping shot tipped away by Robinson.
18mins: Kanoute managed to steal a yard on back line onto Mendes pass, dithered a little and tackled by Dunne.
22mins: YELLOW. Fowler up against King and Naybet just outside box, turned inside Naybet, contact made, Naybet booked, Sibierski's free-kick into wall.
25mins: CLOSE. Ball played wide left to Ricketts, took into box, cut between Dunne and Mills, rolled ball wide of James but agonisingly inches from Kanoute's toe and the far post.
39mins: MISS. Keane broke offside trap and onto lovely pass from Mendes, James out to meet him, flicked over keeper but missed target from 12 yards.
42mins: CLOSE. Sibierski diving full length to meet Jordan's deep cross, made it but couldn't guide it on target.
43mins: Mills deep cross headed back towards Fowler by Macken but King in for crucial interception.
Half-time: Manchester City 0, Spurs 0
Half-time: SUBS. Kelly and Gardner for Mendes and Naybet. Kelly in at left-back, Atouba up to left midfield.
52mins: Macken first effort of second half, lashed high and wide.
55mins: Keane backheel released Kanoute, left channel, cut back behind supporting players.
56mins: GOAL. Brown lovely reverse pass over the top to Kanoute, left corner of box, beat Dunne and lashed into top right corner.
Manchester City 0, Spurs 1
64mins: Fowler short corner with Bosvelt, drilled shot from right edge, Robinson held on well with Macken ready to pounce on any spill.
68mins: OFF LINE. Keane onto Kanoute's pass, around James only for Distin to clear off line from tight angle.
71mins: SUBS. Anelka and Bradley Wright-Phillips for Fowler and Macken.
78mins: MISS. Chance to wrap it up as Brown dispossessed Distin, sprinted into box, squared to supporting Keane who somehow cleared crossbar from five yards.
81mins: SUB. Redknapp for Ricketts.
Final score: Manchester City 0, Spurs 1
Line-ups: Manchester City: James, Distin, Mills, Jordan, Dunne, Barton, Bosvelt, S Wright-Phillips, Sibierski, Fowler (B Wright-Phillips, 71), Macken (Anelka, 71). Subs: Waterreus, Onuoha, Flood.
Spurs (4-4-2): Robinson; Pamarot, Naybet (Gardner, 45), King, Atouba; Brown, Carrick, Mendes (Kelly, 45), Ricketts (Redknapp, 81); Keane, Kanoute. Subs: Fulop, Yeates.
Referee: Dermot Gallagher.
Fredi Kanoute's magnificent strike secured a deserved win at Manchester City and our third on the trot in the Barclays Premiership on Saturday.