The South African, on his return from six weeks on the sidelines, cushioned Kevin Mirallas' low cross into the far corner with his first touch to seal all three points.
His goal proved the decider in a game in which Mirallas had seen his early strike cancelled out by Yannick Sagbo.
Pienaar's winner just before the hour mark ended the Tigers' four-match unbeaten run while Everton moved up to fifth spot in the Premier League standings.
Pienaar, whose last appearance before a hamstring injury was on August 31, made a timely return after the loss of fellow midfielder Darron Gibson to an anterior cruciate ligament rupture this week.
His intervention was particularly welcome for Everton as, having lost the only remaining unbeaten league record at Manchester City prior to the international break, they appeared in danger of throwing away their early advantage.
Mirallas put them ahead in the eighth minute but Hull could have a valid argument for it being disallowed.
At first glance it seemed Allan McGregor appeared to leave the Belgium international's low shot just before it cannoned off the inside of his right-hand post.
However, replays showed Gareth Barry was running back from an offside position and even tried to backheel the ball as it went past him and so the Hull goalkeeper could be given the benefit of the doubt.
It was the first Premier League goal at the Gwladys Street End since Mirallas scored against West Ham on May 12 and the first Hull had conceded in 232 minutes of league football.
If Hull were a touch unfortunate with the goal their luck worsened in the 15th minute when they lost Danny Graham, still desperately seeking his first goal for the club, to injury.
Strangely his loss appeared to galvanise the Tigers and centre-back Abdoulaye Faye twice failed to capitalise on good headed chances from corners, the second after Sylvain Distin's overhit knee-high backpass was sliced into the Park End by Tim Howard.
Having escaped sanction earlier, Barry was booked for going over the top in a challenge with Sone Aluko and, despite having just clipped the top of the ball, other referees may not have been as lenient as Neil Swarbrick.
Aluko showed no ill-effects, however, as he returned to the action to immediately set up the equaliser having beaten Leighton Baines to the byline to cross for Sagbo to convert first-time at the near post.
Mirallas continued to be Everton's best attacking outlet after the break though and it was he who provided the pin-point cross to set up Pienaar's goal.
Pienaar, who had missed four league matches with a hamstring problem, deserves huge credit for the quality of the finish though as he brilliantly steered home.
The fight should have been knocked out of Hull in the 76th minute when Arouna Kone, on for a subdued Romelu Lukaku, did brilliantly in dropping his shoulder to wrongfoot Faye but with just McGregor to beat from close range he somehow managed to crash his shot against the post.