Early goals from Izale McLeod and Gabor Gyepes had put Pompey firmly in charge but Adam Webster's own-goal and Potter's 72nd minute tap-in stretched the Dons' unbeaten run to six games.
Portsmouth tore the Dons apart early on and Brian Howard fired a penalty against the post in the fourth minute after McLeod had been brought down in the box by keeper David Martin.
But McLeod netted against his former club just a minute later when he burst past two Dons defenders and slotted the ball past Martin one-on-one for his fifth goal of the season.
Wes Thomas then had a strong penalty appeal waved away after he appeared to be tripped in the box by Shaun Williams before an unmarked Gypes nodded in Howard's free-kick to make it 2-0 - his third goal in three games.
The Dons were handed a lifeline five minutes before the break when Webster miscued Dean Bowditch's cross into his own net. They seized control after the interval and Potter equalised in the 72nd minute, scrambling the ball in from close range after Dean Lewington's header had come back off the crossbar.