The former St Mirren marksman pounced on David Clarkson's pinpoint pass to turn and drive in a late winner for the UEFA Cup-bound side.
Neither team created many clear-cut opportunities during a dour match which only came to life in flashes and Hibs were left again to rue a failure to turn glimpses of the target into goals.
Scotland manager George Burley watched from the stands along with Celtic boss Gordon Strachan but neither would have been too impressed with the fare on show.
Home keeper Yves Ma-Kalambay would have been glad to get a couple of early touches as he made his first appearance for Hibs since last season due to his stint at the Olympics with Belgium.
However, the former Chelsea youngster would have been less pleased when he spilled a high ball under pressure from the Motherwell attack in the sixth minute.
Two minutes earlier, the Easter Road hosts carved out the first opportunity of a cagey contest.
Steven Fletcher's intelligent flick was perfect for Dean Shiels on the right side of the box but, when he shrugged aside Mark Reynolds' challenge, keeper Graeme Smith was alert to the danger and blocked with his midriff.
Motherwell enjoyed their fair share of possession without troubling Ma-Kalambay too greatly, despite some penetrating balls into the penalty area.
Fletcher, still seeking his first goal since March, looked to have passed up another gilt-edged opportunity at the other end in the 19th minute as he scooped over from eight yards but referee Stuart Dougal spotted a handball from the striker.
On the half-hour mark, Ma-Kalambay was forced into his first save of the game when Stephen Hughes was left in acres of space 30 yards out and drove powerfully towards the roof of the net.
The home number one dealt less competently with the resultant corner, however, as he flapped at the ball in attempting to punch clear.
Motherwell had plenty of the ball at this stage without creating much in the final third of the pitch, in contrast to the home team, who swung to the other end and threatened the deadlock.
Shiels beat Stephen Craigan to a long ball and outwitted his Northern Ireland team-mate only to see Smith beat his shot away and a defender get in the way of his follow-up effort.
With two minutes remaining of the half, it was the offside flag that denied the home team as Fletcher headed in Shiels' cross from close range.
It was Motherwell's turn to waste a chance just after the break as Steven McGarry crossed from the right only for Sutton to scoop his header over unmarked from 10 yards out.
The match burst to life at this point and briefly swung from end to end, with Ma-Kalambay having to look smart to block at the feet of Keith Lasley as the Fir Park visitors sparked a counter-attack.
Referee Dougal was then put on the spot as Chris Porter crashed to the ground with his back to goal four yards out but the official waved aside the visitors' penalty claims.
With time running out, the visitors finally made the breakthrough.
Clarkson finally found space after an afternoon tightly marked by Ian Murray and he threaded a pass into the area.
Sutton, with his back to goal, made the most of the space he was granted by the home defence to turn and rifle his shot into the roof of the net from 12 yards out.
Hibs fired high balls forward in the closing stages but their hopes of snatching a draw drifted away as referee Dougal waved away substitute Steven Pinau's appeals for an injury-time spot-kick.