Wednesday went ahead in the first half and it took until half way through the second for Town to get there stride.
A Greg Kelly goal on 64 minutes put The Terriers back on level grounds, and it was half time subtitute John McAliskey, on his return from 14 months out with a back injury, that scored the Terriers winning goal.
It was from a well worked free-kick that the tall centre forward hammered the ball in to the back of the net from close range.
Academy director Gerry Murphy prasied the second half performance, 'We did not play to well in the first half, they scored first and we couldn't equalize beacause we wern't playing too well.'
'We were alot better in the second half, superb at time and i was extremley pleased at both our goals. It was good to see John get a goal too after so long out.'
Bad news for the Academy is that Joe Washington broke his leg on Saturday and will be out for some considerable time.