Debutant Walker's 82nd-minute strike did the trick as the Championship side avoided an upset against their League One hosts at the Stadium:mk.
Defender Declan Drysdale was shown a straight red card in the 27th minute for a needless foul on Matthew Sorinola.
But the hosts failed to take advantage and Slovakian goalkeeper Marko Marosi produced a fine save to deny Carlton Morris from the resulting penalty.
Marosi also denied Morris from close-range in the second minute, while the striker later blazed over the bar when well placed.
MK Dons wasted further chances in the second half before Giles' ball into the box was not cleared and substitute Walker converted, while Coventry's Amadou Bakayoko also hit a post it the dying stages.