Boro looked set to follow promotion rivals Cardiff and Crystal Palace in dropping points before the game turned two minutes from time when a Scott McDonald cross hit Karl Henry on the arm.
The linesman pointed to the spot and the referee gave the penalty, which Marvin Emnes slammed home before McDonald struck deep in stoppage-time.
Wolves boss Stale Solbakken fumed at the final whistle but Mowbray, whose side are now just a point behind second-placed Palace, was satisfied justice had been done.
"I'm not going to question the integrity of the officials, they call it honestly every game," said the Boro manager.
"The boy leant into the ball and that's why the linesman called it how he did.
"It was a huge result for us. It wasn't the most fluid or polished we have played all season but that doesn't matter now.
"We can't play well every week but it wasn't exactly daylight robbery. We worked hard and kept going and I think we got our rewards."