Akins curled in his fifth goal of the season in the first half and Boro repelled a second-half onslaught to end the Dons' seven-match unbeaten run.
Stevenage had the better of the first half and Akins put them ahead after 27 minutes, cutting inside Luke Chadwick to curl a fine shot past David Martin from the edge of the box.
Akins almost doubled their lead moments later with a fierce low volley but Martin produced an excellent reflex save to keep it out with his boot.
The Dons largely lacked a cutting edge in the first half but Boro keeper Steve Arnold twice denied Chadwick and tipped wide a 25-yard drive from Stephen Gleeson.
The hosts seized control after the break and Darren Potter missed two good chances to equalise, first when he headed straight at Arnold and then when he sliced a half-volley well wide. Arnold then denied Dean Lewington and Scott Allan, while Akins and Marcus Haber both had efforts cleared off line for Boro on the counter-attack late on.