The Nigerian striker could barely miss from six yards after fine work from Lumana Lualua to finally beat Paul Robinson.
The winner arrived after 62 minutes and followed our best spell in the match - a five-minute period that saw Anthony Gardner hit the post and Shaka Hislop tip Jermain Defoe's shot over.
We finished with a fight in injury time as Johnnie Jackson's goalbound shot was blocked and Noureddine Naybet flicked a header wide but, in truth, it was difficult to argue with the result.
Pompey had much the better of the first half and England number one Robinson had to be at his best to keep the home side out.
He denied Yakubu in the tenth minute with a superb one-on-one save low to his right and bettered that to tip over Eyal Berkovic's shot after 23 minutes.
Throw in how he somehow managed to claw Patrick Berger's header across goal away from Lualua and a save from Nigel Quashie's tricky low drive that he made like shelling peas and you could see why there was hope for us going into the second half on level terms.
That hope looked like it might turn into goals when Gardner met Michael Brown's free-kick in the 53rd minute only for it to cannon back off the post and when Hislop flicked Defoe's shot over, the game looked to be turning in our favour.
It wasn't to be though as Lualua skipped down the right and stood up a superb cross that Yakubu couldn't miss.
Michael Carrick came on for his debut alongside Fredi Kanoute but there was little in terms of chances for until the injury time flourish.
MINUTE BY MINUTE GUIDE
4mins: Berkovic fed Lualua, break down left, cross deflected into Robinson's hands.
6mins: Davies side-foot volley from Mendes pass, 18 yards out, comfortable for Hislop.
7mins: Mendes fired over from 25 yards.
10mins: Great diagonal run into box from Davies from right flank, spotted by Mendes, flicked header over.
10mins: SAVE/MISS. Berger's pass found it's way through to Yakubu, in box, Robinson superb low save to his right one-on-one, Berkovic following up with more or less open goal, volleyed over from 15 yards.
13mins: Quashie low drive from 25 yards, Robinson made tricky save to his right look easy.
21mins: Lualua pass into Yakubu, Pamarot pushed for offside flag that never came, Yakubu would have been through but poor first touch took ball straight to Robinson.
23mins: SAVE. Berger break into box, King and Naybet blocked shot, ball out to Berkovic on 18-yard line, Robinson tipped over.
28mins: Tricky ball into box half-cleared, Gardner did well to flick ball away from Lualua.
30mins: SAVE. Berkovic dinked free-kick into box, Berger headed back across goal, Robinson at full stretch touched ball away from Lualua and took nasty hit in the process.
35mins: Keane worked a yard of space 30 yards out, didn't really get hold of shot, dragged across goal.
45mins: TACKLE. Our best move of the half, Mendes into Defoe, he spun and attacked Primus, played one-two with Keane, looked set to finish but Stefanovic managed to take ball off his toe.
Half-time: Portsmouth 0, Spurs 0
49mins: Davies fizzed ball across six-yard line from right flank but too quick for Atouba at far post.
51mins: Lualua pace past Naybet down left flank and into box, cutback too deep for Yakubu and Berkovic made hash of shot from 18 yards.
53mins: SAVE. Slick passing between Brown, Mendes and Davies, Davies laid ball into Defoe, shot from 16 yards deflected by Primus and tipped over by Hislop.
54mins: WOODWORK. Brown floated in free-kick from central position, Gardner in from left angle to header against the foot of the post. Defoe onto rebound but defenders back to block.
54mins: CLOSE. Best spell of pressure now, Defoe snapshot from 18 yards just over.
55mins: SUB. Fuller for Berkovic.
58mins: Berger worked shooting chance, 18 yards out, dragged across goal - might have done better.
62mins: GOAL. Lualua to byline, stood up perfect cross for Yakubu to head home from close range. 0-1.
Portsmouth 1, Spurs 0
72mins: SUBS: Kanoute and Carrick for Gardner and Brown.
74mins: Kanoute header from Davies cross always going over.
75mins: Kamara for Yakubu.
79mins: SUB. Jackson for injured Atouba.
82mins: CHANCE. Ball bounced around, fell to Kamara, 15 yards out, snatched shot wide.
84mins: SUB. Cisse for Berger.
88mins: Keane shot straight at Hislop from 18 yards.
Injury time: PENALTY?/BLOCK. Appeals for handball as Kanoute headed at goal, ball fell nicely to Jackson's left foot but goalbound shot blocked by Primus.
Injury time: CLOSE. Naybet glanced Keane's corner just wide.
Full-time: Portsmouth 1, Spurs 0
Line-ups: Portsmouth: Hislop, Griffin, Stefanovic, Primus, Unsworth, Berger (Cisse, 84), Quashie, Faye, Berkovic (Fuller, 55), Yakubu (Kamara, 75), Lualua. Unused subs: Ashdown, Taylor.
Spurs (expected 4-4-2): Robinson; Pamarot, King (captain), Naybet, Gardner (Carrick, 72); Davies, Mendes, Brown (Kanoute, 72), Atouba (Jackson, 79); Keane, Defoe. Unused subs: Keller, Ziegler.
Yakubu Ayegbeni's second half header ended our unbeaten run on the road as Portsmouth won Monday night's clash 1-0 at Fratton Park.