Second-half goals from Mathias Doumbe and Angelo Balanta were enough to seal a comfortable win.
Brentford keeper Richard Lee did well to tip Balanta’s 57th-minute drive around the post but from the corner that followed Doumbe rose unmarked to power home a header.
Three minutes later the visitors doubled their lead when Balanta found himself in acres of space to slam an unstoppable volley inside the post from 20 yards.
To add to the Bees’ misery Pim Balkestein saw red late on after picking up two yellow cards in as many minutes.
It was no more than MK Dons deserved after Balanta had also seen a curling drive cannon to safety off the outside of the post on the stroke of half-time.