Owusu nodded home Jay Tabb's cross in the eighth minute to see off the plucky Dons, who were left to rue Izale McLeod's 85th minute penalty miss.
Dons manager Danny Wilson made four changes to the team that lost 3-0 at Nottingham Forest on Saturday with Wade Small, McLeod, Nicky Rizzo and Leon Crooks back in the line-up.
Gareth Edds missed out with a heel injury and Dean Lewington was suspended, while Ben Harding and Scott Taylor were dropped to the bench.
Brentford started strongly and Jamie Smith got round the back of the Dons' defence in the second minute, but Darren Pratley's header from his cross looped just over the bar from nine yards.
The Dons struggled to get into their stride but Rizzo's cross-shot was tipped around the post by Brentford goalkeeper Stuart Nelson, before Owusu put the Bees ahead at the other end in the eighth minute.
Trent McClenahan's weak back-header was intercepted by Jay Tabb, who unselfishly lifted the ball across on-rushing Dons' keeper Ricardo Batista for Owusu to nod into the open goal from close range.
The fired-up Bees stepped up a gear and Owusu stung Batista's hands from long range before Paul Brooker blazed woefully wide after Crooks' slip had put him clean through in the 13th minute.
At the other end, McLeod should have equalised for the Dons but he missed his kick from four yards as Rizzo's low free-kick fizzed across the face of goal in the 17th minute.
Brentford continued to dominate with a strong wind on their backs and Tabb's angled drive from the edge of the box was deflected just over the bar in the 38th minute.
But the unlucky David Partridge headed against the bar for the Dons four minutes before the break, after Gary Smith's whipped corner had been flicked on by Ben Chorley at the near post.
And then Bees' centre-half Michael Turner's powerful header from Steve Brooker's corner was beaten out by Dons' keeper Batista as the visitors ended the first half on top.
Owusu lashed Callum Willock's pull-back wildly over the bar from close range for the visitors five minutes after the break, before McLeod controlled McClenahan's cross in the box and poked the ball against the post for the Dons six minutes later.
Dons' substitute Malvin Kamara's low angled drive was saved well one-handed by keeper Nelson in the 72nd minute as the improved Dons pressed for an equaliser late on.
And the inspired Nelson kept out McLeod's header from a yard and tipped Rizzo's rasping 25-yard drive wide, before McLeod somehow failed to connect
with Smith's teasing free-kick from just four yards out.
But the Dons were thrown a lifeline when McLeod was brought down in the box by Smith in the 84th minute.
Yet the mis-firing McLeod completed a miserable day personally and for the Dons by smashing the resulting penalty against the bar five minutes from the end.