Anthony Knockaert had given Brighton the lead on 82 minutes after pouncing on a loose ball as the Toffees looked to be heading to another defeat.
But Rooney scored a penalty in injury time to ensure Koeman’s side left the Amex with a point.
The former England international was given the opportunity to rescue his side a point after team-mate Dominic Calvert-Lewin received an elbow to the face from Brighton defender Bruno in the box as a free-click was floated in.
Up stepped Rooney to send Mat Ryan the wrong way but the goalkeeper saved his side twice in the dying seconds after Kevin Mirallas had his efforts saved.
The game was far from entertaining though and Koeman remains a boss under pressure to get results.
Everton remain just two points above the drop zone and the Dutchman is still the favourite with the bookies to be the next Premier League manager axed.
Up next for Everton is Lyon in the Europa League on Thursday before back to back Premier League matches against Arsenal and Chelsea.
Koeman needed a big win against the Seagulls to relieve some pressure from the fans but today’s performance was anything but convincing.
Both teams move to eight points with Brighton 13th and Everton now 16th.
FULL MATCH REPORT TO FOLLOW.