Top-scorer Nicky Forster scored the only goal of the game in the second half to give the South Coast club their fifth win out of seven.
The decisive moment of the match on a rain-drenched afternoon at Withdean was shrouded in controversy.
Forster appeared to be tripped from behind by Brian Stock as he ran into the box. The referee pointed to the spot, to the disgust of the Rovers players.
Stock was booked before Forster's penalty was saved by Neil Sullivan, but the ball came back out for Brighton's experienced striker to convert his 16th goal of the season on the rebound.
Forster admitted afterwards: "It was a soft penalty. Strikers sometimes go down when they're running at pace.
"I don't consider myself a cheat and I didn't dive but I didn't appeal. There wasn't much contact."
Despite the disputed fashion of only their second defeat in 15 away games, Doncaster could have no real complaints.
Brighton were the better side apart from the opening 20 minutes when Rovers threatened to take a grip on the game and Stock struck the bar from close range.
Paul Heffernan also missed the target with a header but Brighton had the edge once manager Dean Wilkins switched to a diamond formation in midfield to combat Rovers' initial superiority.
Doncaster's former Leeds and Scotland goalkeeper Sullivan was equal to the task and he kept Rovers' hopes alive after Forster's breakthrough with a smart double-save which denied Ian Westlake and Glenn Murray.
Doncaster chief Sean O'Driscoll made a triple substitution with 15 minutes left but it made no difference and Brighton should have scored a second goal in the closing stages.
Gary Hart, on in place of Forster, was put clean through by Dean Cox but shot tamely at Sullivan.