Malbranque headed Tottenham level early in the second half to scrub out Benjani's deflected first-half effort.
Andy Cole's reward for scoring his third goal of the season at Bolton on Saturday was being dropped to the bench as Harry Redknapp recalled regular strike pair Nwankwo Kanu and Benjani.
Jol axed Egyptian striker Mido and Ivory Coast midfielder Didier Zokora following their 1-0 defeat at home to Liverpool, with Teemu Tainio and flu victim Dmitar Berbatov recalled.
Spurs were without the crocked Jermaine Jenas and Ledley King and the visitors' injury problems deepened when Hossam Ghaly was left with blood pouring from his head after being kicked in the face by Noe Pamarot after only two minutes.
Berbatov almost drew first blood for Spurs when he headed two yards over from Tom Huddlestone's resulting free-kick.
David James was forced to come racing out of his goal to save at the feet of former England team-mate Jermain Defoe seven minutes later after the quick-fire striker had raced onto Berbatov's knock-down.
Pompey had to make an early substitution when Pamarot hobbled off with a groin injury against his old club to be replaced by Croatian Niko Kranjcar in the 12th minute.
In-form Matt Taylor came to Pompey's rescue soon after, sliding in to nip the ball off the feet of Malbranque after Berbatov had driven in an inviting left-wing cross.
Benjani put Pompey in front against the run of play in the 29th minute with his fourth goal of the campaign. Substitute Kranjcar threaded through a lovely left-footed pass before Benjani unleashed a 20-yard curler, which took a wicked deflection of the grounded Calum Davenport and flew past Paul Robinson and into the left-hand corner.
Jol called Danny Murphy from the bench at half-time in place of the ineffective and wounded Ghaly to add some extra spark to the Spurs attack.
That move almost paid dividends straight after the restart as Huddlestone hooked in an inviting cross for Berbatov at the back post.
The Bulgarian drilled in a fierce volley across James' goal but the veteran keeper came flying across his line to pull off a brilliant two-handed save and push the ball behind.
Spurs drew themselves level within five minutes of the second half, with Murphy at the centre of Malbranque's equalising strike.
The former Liverpool midfielder whipped in a deep left-wing cross and the Pompey defence allowed Malbranque to head home unchallenged at James' left-hand post.
Pompey almost hit back two minutes later when the Spurs defence failed to deal with a Taylor corner. Taylor picked out Benjani at the back post and his header found Kanu but the giant Nigerian put two shots wide of Robinson's goal.
James was Pompey's hero twice in the space of two minutes midway through the half. First he denied Defoe with a smart stop after Tottenham's top scorer had cut in from the left and fired in a right-foot pile-driver from 16 yards.
James then got down low to his right to claw Huddlestone's half-volley off the line. Linvoy Primus could have won it for the home side late on when he headed inches wide after latching onto Taylor's free-kick.