The home side almost took a third-minute lead when Mark Duffy floated his free-kick inches wide of the near post, but Brighton opened the scoring in the eight-minute when midfielder Jake Forster-Caskey sent a thunderous 35-yard strike into the top corner.
The second half descended into a scrappy affair, as neither side managed to carve out any chances.
However, Doncaster did find a way back into the game when Chris Brown converted Duffy's free kick after 75 minutes.
Ashley Barnes almost struck back immediately for the Seagulls, but his shot rebounded back off the post.
With the game seemingly drifting towards a draw, substitute Leroy Lita pounced to slot home an 85th-minute goal from Barnes's overhead kick.
In stoppage time, fellow replacement David Lopez ensured the victory with a free kick.