The striker, who had opened the scoring in the 12th minute of Saturday's Scottish Premiership clash, headed home from close range to deny Hibs after the home side had come back from 2-0 down.
Hibs started this thrilling contest brightly but fell behind in the 12th minute against the run of play. James McFadden played in Lionel Ainsworth down the left flank and the forward's low pass across goal was placed into the net by the unmarked Sutton at the back post.
Motherwell doubled their advantaged in the 29th minute with a brilliant individual effort from Ainsworth. The on-loan Rotherham forward accepted a pass from Keith Lasley, effortlessly nutmegged Michael Nelson and curled a sublime 18-yard effort into the top corner of the net from 18 yards.
The visitors had looked comfortable but Hibs managed to reduce their arrears two minutes before the break when Jordan Forster headed home Paul Cairney's corner.
The home side levelled in the 76th minute in controversial circumstances. Cairney's corner was met at a congested back post by Nelson and the defender's downward header bounced off the underside of the bar.
Motherwell thought they had successfully cleared the danger but referee Steven McLean awarded a goal.
Hibs stormed ahead in the 79th minute through Paul Heffernan, just four minutes after he came on as he lifted a shot over Lee Hollis.
The drama was not over there though, with Sutton earning the visitors a point with his second goal in stoppage time, following a scramble inside the six-yard box.