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.
However, the goal is unlikely to lift the pressure on Everton manager Ronald Koeman, whose out-of-sorts side are still without an away win since January.
The under-fire Dutchman's latest bid to solve their goalscoring problems saw him select Rooney in attack, but until the penalty the former England captain had barely had a shot in anger.