Boro took the lead after a fairly even and well contested first half hour, Szilard Nemeth scoring at the second attempt, following a save by ex-Boro keeper Gary Walsh.
Wigan took the game to Boro in the second half but failed to get an equaliser, with David Knight being the busier goalkeeper.
Adam Johnson wrapped up the points following a great three man move, involving Danny Graham and Tom Craddock, finishing well from ten yards.
It was a useful run-out for Riggott, Mendieta and Nemeth ahead of Thursday's trip to Greece. They were all given 45 minutes, while Parnaby played the full game.
Boro team:
Knight, Parnaby, Hines, Cattermole, Riggott (Wheater), Bates, Mendietta (Liddle), Kennedy, Graham, Nemeth (Craddock), Johnson