But the game was marred four minutes from the end by a double dismissal.
The home team's Mark Tinkler and Dons substitute Aaron Wilbraham were shown the red card after an assistant brought the referee's attention to an off-the-ball incident.
Bizarrely, Wilbraham had only been on the pitch for 20 seconds.
MK Dons won three corners in the first three minutes but Pool quickly recovered and on five minutes visiting defender Pablo Mills cleared off his own line as Eifion Williams looked a certain scorer after Jon Daly headed down a cross.
Mills was in action again on 21 minutes when he headed a Chris Llewellyn cross behind for a corner as Williams waited for it at the far post.
And two minutes later Dons got their reward for defending so well when they broke out to score.
Stephen Quinn split a static home defence with a great short pass into the area and Izale McLeod nipped in from the right to slot his shot under the body of home keeper Dimi Konstantopoulos.
The goal gave MK Dons a great lift and on 32 minutes they thought they had a second when McLeod scored from close range but the flag was up for offside.
The best a desperate home side could muster was a shot on the turn from Tony Sweeney seconds before the break but the effort was just off target.
But Pool were level on 50 minutes when Thomas Butler's left-wing cross was turned into his own net at the far post by defender Dean Lewington and the home side had their tails up.
The won the game with just six minutes left when Darren Craddock crossed from the right for substitute Lee Bullock to head powerfully into the corner of the net.
And two minutes later Tinkler and Wilbraham had the last word.