The ex-England captain won his side's first spot-kick after Dean Lewington brought him down in the area in first half injury time. Swindon right-back Jack Smith decided to take the kick after normal penalty taker Christian Roberts decided he didn't want to take one.
Smith hit his penalty into the bottom left-hand corner of the net to make it 1-1.
MK Dons midfielder Jon-Paul McGovern opened the scoring for the visitors with a right-foot volley after the Swindon defence failed to clear a corner.
However following the equaliser Swindon won a second spot-kick on 56 minutes when left-back Lewington brought down Andy Caton in the box with a clumsy challenge.
Midfielder Paul Evans took the kick as Smith had gone off just after half time with a leg injury. Evans drilled home his penalty, although MK Dons goalkeeper Adolfo Baines-Pilart guessed the right way, but he could not keep it out.
Swindon made the game's first chance when Lee Peacock crossed for Caton, but the midfielder could only head wide.
MK Dons hit back with a spell of pressure with Keith Andrews going close with a left-footed shot that whistled passed the post. After the McGovern goal Swindon woke up and got back into the game.
Curtis Weston ran through the MK Dons defence and put his shot just wide of the left-hand post. After Swindon went ahead with the two penalties either side of half time, the rest of the game belonged to the MK Dons. They put constant pressure on the Swindon defence but could not find a way through.
Jerel Ifil held firm at the rear and headed away everything that was thrown at him.
Centre-back Ben Chorley came closest to getting the equaliser when he hit the bar with a left-footed volley from 25 yards with keeper Petr Brezovan well beaten.