The 27-year-old, signed from Swindon two years ago, had managed just one goal for the club prior to this Championship clash and, when he was announced as one of five changes made by Warnock following defeat to Derby on Monday, his name was greeted with sarcastic cheers from fans who had grown tired of waiting for him to prove his worth.
He answered them, though, scoring twice as Warnock's men replied to Joe Newell's opener in some style, with Ross McCormack also grabbing a brace to take his tally for the season to 19.
Paynter's first and McCormack's double came in a chaotic 180-second burst either side of the interval and killed off a Posh side who are still not mathematically safe from relegation and require a point to survive.
Today was Paynter's day, however, and after being handed a rare start ahead of Luciano Becchio, he set about proving to Warnock that he wants to remain in a squad that the veteran boss has repeatedly stated since his February arrival needs major surgery.
He had a first-minute one-on-one saved and then had a second-minute header cleared off the line, while Robert Snodgrass was also denied under the bar as Leeds looked to have heeded Warnock's post-Derby warning that one of his sides would never play so badly again.
That quickly looked likely to be a false statement, though, as Posh got on top.
George Boyd missed two presentable chances, one after Andy Lonergan came for and missed a cross, the other after teenage defender Charlie Taylor slipped and lost possession.
Leigh Bromby's deflected header then clipped Peterborough's bar, but Leeds looked shaky at the back and, after another Taylor error, the visitors took the lead when Newell robbed him of possession in the 37th minute and tucked under Lonergan from an acute angle.
Boyd should have made it two seconds later but could not adjust his feet after the home keeper shelled Paul Taylor's shot, meaning that when Paynter scored from a yard in first-half injury time after Paul Jones dropped a Snodgrass shot, it brought Leeds level rather than giving them a lifeline.
If Peterborough were stunned by the goal then they were even more shellshocked after the break as McCormack's quickfire double put them out of sight.
First, his weak back-post volley after a Paynter flick somehow bobbled over the top of Jones and then, as Peterborough poured forward, Snodgrass, Danny Webber and Adam Clayton picked them apart to give the Scot a two-yard tap-in.
The game was over as a contest now and Leeds probed for chances seemingly at will, with Paynter taking one with 17 minutes left.
Tom Lees' cross found its way to him at the back post and his clinical 12-yard finish belied a man who only 40 minutes previous had scored his maiden home goal for the club.
He could and should have had a hat-trick after that, blazing wide when played in by Webber, before Warnock afforded him a standing ovation when he withdrew him with seconds remaining.