Crewe took an early lead as Shaun Miller steered in the opener from a Luke Murphy pass.
The lead only lasted a minute as the Brewers hit back as John McGrath fed Shaun Harrad who scored from 15 yards out.
Harrad hit the post in the second half, forcing goalkeeper Steve Phillips to make the safe.
But it was Donaldson who came off the bench to grab a late winner as Crewe ended Burton’s five-game unbeaten run in a 2-1 home defeat.
