Brian McBride rescued a point late on for Fulham after Yakubu had put Portsmouth ahead as the hosts all-but secured their Premiership status.
Lomano LuaLua shot wide before crossing for Yakubu to head over as Pompey made the brighter start at Fratton Park.
LuaLua dragged another effort wide before Sean Davis struck the bar with a fierce drive as Fulham threatened.
Yakubu thought he had won it by tapping home Matt Taylor's cross but McBride levelled with a fine left-foot strike.
Portsmouth needed just a point to make sure of their Premiership status and LuaLua shot wide before Nigel Quashie's goalbound drive was blocked by Alain Goma.
Fulham responded with Luis Boa Morte forcing a comfortable save low down from Shaka Hislop, but it was Pompey who were doing most of the pressing.
LuaLua found some space down the right and crossed onto the head of Yakubu, but the in-form Nigerian could only direct his weak effort over the bar from six yards.
Alexei Smertin was controlling the midfield for the home side, prompting and probing and always looking for a chance to use the pace of LuaLua and Yakubu.
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KEY MOMENTS
17 mins: Yakubu heads over from LuaLua's cross
46 mins: Davis crashes a shot off the underside of the bar
80 mins: Yakubu nets opener
85 mins: McBride equalises
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LuaLua again found himself in a good but dragged his shot across goal from six yards out, before the DR Congo striker forced Van der Sar to parry away a thundering effort from a near-impossible angle.
Fulham were struggling to keep the rampant hosts at bay, and Sylvain Legwinski and Carlos Bocanegra were cautioned late on in the first half for late challenges.
Fulham had failed to create one good opening, but it took them just 18 seconds after the break to threaten, Davis crashing a right-foot shot against off the bar with Hislop beaten.
Pompey quickly reponded when Steve Stone's cross was volleyed wide by Yakubu after great work from Smertin, before Boa Morte headed wide at the other end.
The game was swinging from end-to-end but Fulham looked sharper, sensing a chance to bag all three points in their push for a European place.
Legwinski blazed over from outside the area while Junichi Inamoto saw one effort blocked by Richard Duffy and another sail wide of the right-hand post.
Portsmouth grabbed the lead when Taylor crossed from the right and Yakubu was on hand to steer the ball home.
But Fulham earned a point just five minutes from time when McBride lashed in a glorious left-foot strike from 25 yards.
The draw leaves Portsmouth nine points ahead of Leeds with the Yorkshire club having three games left, but with a goal difference 26 inferior to Harry Redknapp's men.
Portsmouth: Hislop, Primus (Duffy 22), Stefanovic, De Zeeuw,
Taylor, Smertin, Faye, Quashie, Stone, LuaLua,
Yakubu (Sheringham 90).
Subs not used: Wapenaar, Berkovic, Harper.
Booked: Faye.
Fulham: Van der Sar, Volz, Goma, Pearce, Bocanegra, Inamoto,
Legwinski, Malbranque, Djetou (McBride 77), Sean Davis,
Boa Morte (John 85).
Subs not used: Crossley, Petta, Hudson.
Booked: Legwinski, Bocanegra, Inamoto, Goma.
Attendance: 20,065.
Referee: S Dunn (Gloucestershire).