Maurice Malpas' side were reduced to nine men as Phil Jevons converted two penalties for Huddersfield Town after Swindon raced into an early three-goal lead.
Referee Ray Lee had to be led away by security as furious Swindon fans barracked the Ipswich official following a highly suspect display.
The game had begun swimmingly for Swindon as they reversed their recent lack of goals with a quickfire treble inside little over half an hour.
Striker Simon Cox broke down the left-hand side after being freed by Anthony McNamee and crossed for Paynter to finish with some class, caressing a half-volley into the far corner of Matt Glennon's goal.
Huddersfield looked out of sorts and the Robins capitalised on some more inept defending to give themselves a two-goal advantage, as McNamee's trickery down the left-hand side found Craig Easton unmarked to slot home with conviction.
Scottish midfielder Easton then scored his second after being found by Paynter in similar amounts of space. Huddersfield midfielder Michael Collins did track back to make a last-ditch tackle, but the ball spooned off his leg and over Glennon to give the hosts a seemingly impregnable lead.
Huddersfield were handed a glimmer of hope just before the break when referee Lee adjudged Miguel Comminges to have clattered Collins on the Swindon touchline when it looked more like a corner.
That was of no interest to Jevons as he confidently stepped up and slotted home the penalty to send his side in buoyant at half-time.
The second half proved considerably different to the free-flowing football of the first, as Peacock received his marching orders for a nasty challenge on Malvin Kamara, before Paynter saw red 13 minutes from time after keeping Andy Booth's goalbound header from going in with his hands.
Jevons was called upon again to convert from 12 yards, but nine-man Swindon withstood a late barrage by the Terriers to ensure all three points and maintain their interest in the final quarter of the season.