The home side started the better of the two sides with Chris Porter having a close-range effort blocked by Rob Jones in the opening minute.
The goal was only delayed by a further minute when a long crossfield ball from Paul Quinn sailed over the head of Hibs right-back Martin Canning, which allowed David Clarkson to sneak in behind him.
The striker took one touch on his chest before bending a shot wide of Andrew McNeil.
Well went on to dominate the opening half and were unlucky not to make it two on a number of occasions, particularly when Quinn fired over and Bob Malcolm headed wide.
They almost paid for these misses on the half-hour mark when a half cleared free-kick found Dean Shiels at the edge of the box, but his shot bounced clear off the crossbar.
The second half started with Motherwell pushing forward once again and within seven minutes Quinn had glanced a near-post header wide.
Twenty minutes later Keith Lasley fired a shot just wide of the right-hand post.
It took Hibs until the 78th minute to muster a shot at goal, with Ian Murray sending a 30-yarder just over.
Four minutes later they did force a save from home keeper Graeme Smith when sub Clayton Donaldson forced him to save his angled drive.
In the end the Steelmen held on to secure their first win since the end of February and keep the pressure on the visitors as they both chase that third-placed finish.