Brighton manager Chris Hughton was left to rue missed chances as Everton scored a late equaliser to draw 1-1 at the Amex Stadium.
The struggling Toffees were staring at another defeat when Anthony Knockaert fired Brighton ahead eight minutes from time.
But Seagulls captain Bruno was penalised for fouling Dominic Calvert-Lewin with two minutes remaining and Rooney tucked home the equaliser.
“To concede so late, it’s even more disappointing,” Hughton told Match of the Day.
“We were the side more likely to score and that we did. I just felt in general play, even with their quality, they wouldn’t carve us open.
“If you don’t put chances away then what happened can happen. We learned that the first game of the season and that was again the case.
“In credit to Bruno, he has had a lot of aerial duels in that second half and generally used his body well. He looked at another opportunity to impede him a little bit, but the referee was right there.
“Generally because there was a little bit of pushing, the referee was on his case more than he may have been.
“We have been in every game and are going to have to play at a certain level – if you play below that you’ll get beat. For large parts of the season we have been.”