Kyle McFarlane (pictured) had fired Blues into a 25th minute lead, before McDonald struck twice. His first arrived just before half-time and his second in stoppage time at the end of the match.
Academy coach Steve Spooner felt his side were good value for their win.
“It was a good performance and every single one of the players played their part,” he said.
“We were right at it. We passed the ball well, got close to people and played at a high tempo.
“It was a fair result, particularly with the way we played in the second half when we dominated it, although we didn't work the keeper quite as much as I would have liked.
“But it was a big plus to score three goals away from home and also keep a clean sheet.”