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.
Behind him Gylfi Sigurdsson flitted around creating little, while Calvert-Smith was largely ineffective stationed out on the left wing.
Despite a television-friendly kick-off slot the match was not actually screened anywhere in the UK - although bizarrely it was live in India.
Unfortunately for the viewers on the subcontinent there was little spice until the final 10 minutes of an otherwise forgettable encounter on the south coast.
Sigurdsson did set up one first-half opportunity, combining with Nikola Vlasic before Idrissa Gueye struck a low drive which Mathew Ryan had to tip past his post.
Having soaked up Everton's early pressure Brighton became more adventurous and only a brave goal-line clearance from Michael Keane denied Lewis Dunk from six yards out.
Dunk wanted a penalty but the ball clearly hit Keane's chest first as he slid in to clear.
In the second half Everton right-back Mason Holgate darted into the penalty area and his fierce cross-shot was palmed away by Ryan.
Calvert-Lewin then planted a header straight at Ryan before Vlasic turned Davy Propper on the edge of the area, only to slice his shot horribly wide.
Koeman's face was a picture of frustration when Calvert-Lewin met Rooney's cross with a weak shot which Ryan dealt with easily.
Frustration turned to despair when lively Brighton sub Jose Izquierdo's drive rebounded into the path of Knockaert, who smashed it past Jordan Pickford to give the hosts the lead.
But Bruno's clumsy elbow into the neck of Calvert-Lewin in a crowded penalty area earned Everton a reprieve as Rooney stepped up to roll in the spot-kick.
The visitors almost snatched a winner at the death but Ryan pulled off a fine double save to deny Kevin Mirallas.