The centre-back, on loan from Fulham, headed home Russell Martin's corner with 13 minutes remaining as Posh pulled themselves back from two goals down.
Rovers' Chris Greenacre took advantage of some poor home defending to open the scoring as he headed the visitors into the lead after seven minutes.
He doubled the visitors' lead on the half-hour mark after rounding Posh goalkeeper Joe Lewis and sliding the ball into an empty net.
Tranmere's star player could have furthered their lead in between his two strikes but Lewis saved well - and that proved costly for Rovers as Posh fought their way back into the game.
Craig Mackail-Smith pulled one back for the hosts when he turned in George Boyd's cross just prior to half-time, before Zakuani completed the fightback late in the second half.