The French midfielder, heavily involved in that second half renaissance, rose unmarked eight yards out to nod home Danny Murphy's cross after 50 minutes.
David James had to be at his best to deny Jermain Defoe and Tom Huddlestone as we recovered from Benjani's opener just before the break to enjoy the better of the second half in the pouring rain on the south coast.
There were two changes to the starting XI from the Liverpool game, with both Dimitar Berbatov and Teemu Tainio restored to the side. Calum Davenport continued to deputise for Ledley King and Hossam Ghaly was assigned the right flank in the absence of Aaron Lennon.
For the home side there were four former Spurs on duty - Sol Campbell, Noe Pamarot, Pedro Mendes and Sean Davis - and Pamarot left his mark on the face of Ghaly in the opening minute with a flying boot in the face of the Egyptian, who suffered a loss of teeth and required stitches.
The first ten minutes were not of a frantic nature although Defoe had the chance to open the scoring when Ghaly did well to nod a long punt into his path and it took a speedy dash off his line by James to stop the striker scoring at the venue where he netted on the first day of last season.
Ghaly came close on 16 minutes when Berbatov galloped down the left and cut the ball back to the midfielder who was knocked out of his stride by a desperate late lunge from Matthew Taylor.
The home crowd came to life after 29 minutes when the lead was secured in fortunate circumstances. Benjani tried his luck from outside the area and his effort kicked up off the closing down Davenport and the ball sailed high past the despairing dive of Paul Robinson. It was not a deserved deficit.
There was a scare just before the break when Campbell struck the bar following a scramble in the six yard box, but the boys will have gone into the interval lamenting their luck over being a goal down in a game which they were bossing to a large extent.
Murphy emerged from the dressing room after the break and took the place of Ghaly - Malbranque switching to the right - in the only half-time change. James made a superb stop to deny Davenport before, four minutes into the half, Murphy made an almost instant impact with a precise centre that left Malbranque with the relatively routine task of nodding into the net.
It was game on and both teams were set on snatching maximum points, although the exchanges became a little scrappy in the wind and rain that was swirling around Fratton Park. James spilt a Defoe effort just short of Berbatov before reacting with an excellent stop to his right hand post to deny a thumping drive from Huddlestone.
Malbranque was replaced by Anthony Gardner with 12 minutes remaining and the tall centre half was quickly in the action with a crucial block in front of Andy Cole before Linvoy Primus went close with a header across the face of goal.
Steed Malbranque headed home from close range to bag the point we richly deserved after our second half display in the 1-1 draw at Fratton Park on New Year's Day.