The popular defender was out of contract in the summer and hadn't played enough games this season to trigger a fresh one.
However, the Blues have stuck by their longest-serving player and rewarded him with a 12-month contract regardless.
It comes after Peter Storrie last week revealed to The News the club would be offering Primus the chance to prolong his eight-year stay.
The 34-year-old has yet to play this season and underwent career-saving knee surgery in January.
His comeback is progressing well and his target of a return to pre-season training on July 1 now looks a reality.
And Primus was quick to thank Pompey for standing by him.
He said: 'I'd like to thank Harry, Peter Storrie and the medical staff who have held my hand throughout my recovery.
'The club have stuck by me, I am very grateful for that, and look forward to playing for Pompey again.'
Primus joined the Blues in the summer of 2000 on a free transfer from Reading.
Since then he's stacked up 218 appearances and established himself as one of the club's best-loved players.
A knee problem had cast doubt over his future after sidelining him for the entire season, with Primus turning 35 in September.
Meanwhile, under terms of his existing deal, Primus had to make 20 appearances for a 12-month extension to kick-in.
But Pompey have waived that stipulation and given him the additional year on precisely the same terms.
He will now be able to push on and put pressure on Sol Campbell and Sylvain Distin for a place in central defence.

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