SHAUN SAIKO'S first goal for the club was not enough as the Academy slipped to their third defeat of the season.
Supersub Stephen Thompson was rewarded with his fifth start of the campaign, while the ever-present Daryl Robson dropped to the bench.
Makeshift striker Richard Langthorne moved back to his more familiar role in the centre of defence, leaving Peter Watling up front as the lone striker.
Boro started the game brightly and looked dangerous on the counter attack through Nathan Fisher and Stephen Thompson.
Yet it was Dave Parnaby's side that went behind after Liam McMenamin's poweful close range volley
But Canadian-born Saiko soon levelled things up.
David Hillerby's 40-yard pass found Jonathan Franks in space on the wing. The youngster then broke free of his marker, cut inside and squared the ball for Saiko to slot home calmly.
But that was as good as it got for Boro as a mixture of defensive mix-ups and a bit of bad luck gifted Wednesday all three points in the second half.
The home side failed to deal with an inswinging corner which hit Nathan Fisher on the side of the head before rolling through Jason Honeyman's legs and into the back of the net.
And there was a fortuitous aspect to Wednesday's third as Andrew Broadbent's long range shot took a huge deflection looping over Jason Steele and into the Boro goal.
Stephen Thompson had a couple of long range efforts but could not reproduce his heroics of last week.
The Academy travel to Nottingham Forest next week.
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