THIS narrow win in their final group game kept Boro's qualification hopes alive as they attempt to reach the knockout stages of the Premier League Cup.
It was the visitors with three clear chances in the opening ten minutes as George Oakley delayed a shot which, when it came, was blocked. The rebound fell to Egli Kaja who brought a terrific one-handed save from Aynsley Pears with a low shot.
Toyosi Olusanya was next with a chance, but with the goal at his mercy he delayed shooting and lost all chance.
After a less than convincing start Boro settled into the game and swept into the lead with 24 minutes played when Alex Pattison stroked home from close range with what was Boro's first real effort of goal.
Boro had a half chance to increase their lead when Marcus Tavernier peeled away at the back post but headed at goalkeeper Nik Tzanev, before Pattison sent a 20-yard free-kick over the bar.
Deep into injury time and just after Oakley had sliced a 20-yard shot horribly wide, Boro had another chance to add a second but Wheatley's low shot was blocked and teammates either side let him know he might have picked them out.
For most of the second half Boro were forced to defend as Wimbledon show3d their determination to get back in the game.
Alfie Egan wasn't far away early in the half, a low shot blocked deep inside the penalty area.
Next it was Kaja who threatened with a shot across the face of goal.
Boro stood firm, but came under increasing pressure and entering injury time Kaja went close again and an Oakley header brought a full-length save away to his right from Pears.
It was a hard-fought win, with Boro completing their group games now sitting in second place, three points behind Fulham and two ahead of Charlton, both of whom have Wimbledon to play in their finals games.
Boro: Pears; Johnson, McGoldrick, Elsdon, Silva Torrajon, Maloney (Liddle 58), Tavernier (Coulson 79), Wheatley (Capt.), Fewster (Soisalo 70), Pattison, Mondal. Subs: Hemming (gk); McGhee.
AFC Wimbledon: Tzanev; Renee-Pringle, Scott, Gallagher, Kalambayi (capt.), Sibbick, Kaja, Egan, Oakley, Olusanya (Antwi 76), Bellikli (Chapman 57). Subs: Bursik, Williams-Bowers, Walker.
Referee: Scott Oldham
Yellow card Fewster 60, foul; Liddle 87, shirt pull.