There were 93 minutes on the clock when the Glovers' former Brentford striker struck his first league goal for his new club, having earlier missed two straightforward headers.
Northampton had dominated the game after Poul Hubertz had cancelled out Justin Cochrane's opener for Yeovil, but they were denied three times by the woodwork.
Gray said: "We totally dominated the second half but we have been done by two long balls down the middle. I was disappointed with our naivety but this game is very cruel and you have to keep your concentration."
Yeovil went in front when a long punt forward by Scott Guyett was headed down by Owusu and Cochrane volleyed his second goal in a week after his summer move from Rotherham.
But the visitors' joy was short-lived as Hubertz fired a left-foot shot under Steve Mildenhall's body.
Andy Kirk went close with an overhead kick which forced Mildenhall into a fine diving save, while Daniel Jones curled a 35-yard free kick which bounced on top of the crossbar before Ryan Gilligan's header was tipped over by Mildenhall.
The second half was sterile for long periods although Andy Holt saw a header clip the crossbar after Kirk's right-wing cross. Then Kirk miscued badly after Chris Doig had a shot blocked.
Yeovil seemed to be settling for a point although Owusu should have done better with a free header from a Ritchie Jones' corner.
Northampton must have known it wasn't their day when substitute Colin Larkin curled a shot against a post and minutes later Owusu pounced to rub salt into the home wounds.