Michael Higdon scored his 20th goal of the season and Dylan McGowan put through his own net to give the Steelmen the lead.
Former Motherwell striker John Sutton pulled a goal back in the second half but the away side held on to secure maximum points to deny Jambos' joint-managers Gary Locke and Darren Murray in the first game since the sacking of John McGlynn.
James McFadden was instrumental in the opening goal, his persistence paying off as his mazy run ended with his ball being deflected into the path of Higdon who fired home from the edge of the penalty area (3).
Stuart McCall's side duly doubled their advantage just five minutes later courtesy of an own goal from the hapless McGowan.
Nicky Law's initial shot was blocked and Australian defender McGowan scored an own goal with a sliced clearance into his own net as he tried to deal with Law's follow-up effort (8).
Hearts rallied without creating too many clearcut chances, although Mehdi Taouil did curl a shot wide of the target as he aimed for the top corner.
Calum Tapping's promising run saw him pass to Jamie Walker but his weak effort barely troubled Well keeper Darren Randolph.
Michael Ngoo finally forced a decent save out of Randolph on 34 minutes following his shot on the turn and Ryan Stevenson was then wayward with his 15-yard drive.
But Hearts stuck to their task and pulled a goal back through Sutton, who headed in a corner from substitute Arvydas Novikovacs (59).
Motherwell boss McCall was left furious though, with the home bench convinced they should have been awarded a throw-in on the halfway line in the build-up to the goal.
Randolph saved a Stevenson shot with his legs as the Jambos pushed for a leveller, while a left-footed half-volley from Andy Webster fell just wide.
But despite their best efforts Hearts failed to grab an equaliser to leave them second-bottom of the table.