The striker, signed from Brentford on Friday as a replacement for Sam Baldock, tapped in the only goal of the game in the 51st minute to condemn Boro to their first league defeat.
The Dons dominated the first half but they struggled to unlock a well-drilled Stevenage defence as Adam Smith, Dean Bowditch and Shaun Williams all blazed speculative long-range shots off target.
The only clear chance of a drab first period fell to Boro midfielder Lawrie Wilson, who fired Byron Harrison’s cutback straight at keeper David Martin following Shaun Williams’ defensive error.
But the Dons upped the tempo after the break and MacDonald put them ahead just six minutes after the re-start, tapping in Luke Chadwick’s unselfish square pass after Stephen Gleeson’s exquisite chip had sent him clear.
Boro piled forward late on in search of an equaliser but Martin tipped over substitute Michael Thalassitis’ dipping drive and Jon Ashton had a header cleared off the line by Chadwick as the Dons hung on.