The Pompey central defender was gifted a straightforward header in the 69th minute after Patrik Berger's corner again exposed Palace's weakness in dealing with corners and set-pieces.
Heavy overnight frost caused a complete layer ice to form over the appalling pitch and delayed the kick off by 40 minutes as the groundsmen worked tirelessly to clear the ice. Despite the bitterly cold conditions the game started in bright sunshine, but it wasn't a bright start to the match.
A stop-start first half saw just one clear cut chance which went to Valery Mezague after 15 minutes. Michael Hughes made a mess of his clearance right on the edge of the penalty box and Yakubu crossed to the unmarked Mezague eight yards out, but he lifted the ball over the bar.
Earlier in the week Velimir Zajec took full-time charge after leading Portsmouth to eight points from their last five matches during his caretaker spell, while Iain Dowie's Eagles recent run is much worse - just three draws from their last seven matches.
Nigerian Yakubu returned to the Pompey starting line up after a long absence with a knee injury, while Dowie fetched in Danny Butterfield for his first game of the season.
In fact Butterfield was behind most of Palace's attacks, giving welcome support to Wayne Routledge.
It was from Butterfield's work that Palace could have gone in front in the opening minute, when his cross had Pompey all over the place. Andy Johnson was poised to slot home until he went down like a sack of potatoes from a Primus challenge but referee Neale Barry saw nothing illegal.
Nigel Quashie, so composed in midfield, tested Gabor Kiraly with a snapshot after Palace fell asleep over a short corner, while at the other end Ben Watson tested Shaka Hislop for the first time after 30 minutes.
After the break Pompey were in complete charge as Palace ran out of ideas fast.
Steve Stone, who did not stop running all afternoon, beat Gonzalo Sorondo and then shot wide of an open goal from ten yards out.
From Berger's resulting corner Kiraly saved Yakubu's header and shortly afterwards Arjan De Zeeuw, just six yards out, hesitated with his shot and didn't get the best of connections and Kiraly saved easily.
Substitute Ricardo Fuller kept the pressure on Palace as he shot wide and minutes later hit the post, before Pompey inevitably opened the scoring after 69 minutes.
Berger's corner found an embarrassing gap in the Palace defence and Primus charged in and headed downwards and beyond Kiraly for an easy goal.
Dowie put the emphasis on all out attack by sending on Dougie Freedman and Wayne Andrews, while defender Fitz Hall moved up front to form a five-man forward line.
Sorondo forced an absolutely brilliant save from Hislop in the dying seconds to ensure Pompey held out for a deserved three points.