Smith, who is expected to be appointed on Wednesday, watched from the stands as Boro won a game that swung on the sending off of Dons defender Mathias Doumbe.
MK Dons broke through in the second minute when Adam Smith’s low cross was pushed out by Stevenage goalkeeper Chris Day to Jay O’Shea and he tapped in.
Boro drew level spectacularly when Michael Bostwick’s first-time effort from 25 yards sped past Dave Martin and into the bottom corner.
Doumbe was then sent off for a second booking and the hosts took advantage straight away as Scott Laird flicked in Luke Freeman’s free-kick.
Three minutes later, Freeman was again the provider as his cross was powerfully headed in by Darius Charles. Any hope offered by Tom Flanagan’s header with five minutes left was quickly snuffed out as Dons defender Gary MacKenzie turned Charles’ cross into his own net.