John Sutton's first-half strike piled further pressure on St Mirren manager Danny Lennon as Motherwell took the three points in Paisley.
The Buddies thought they had won a penalty when Keith Lasley pulled down Conor Newton.
But referee Craig Thomson changed his decision to a free-kick outside the box after consulting his assistant.
A Sutton header squeezed over the line before St Mirren's Gary Harkins had an effort cleared off the line.
The game began tentatively, with both sides unable to maintain possession for any prolonged spell.
Interview - St Mirren manager Danny Lennon
A Steven Thompson header flashed wide of the Motherwell goal from a Gary Teale cross.
At the other end, a searching ball hoisted into the Saints box defied goalkeeper David Cornell and the Well strikers before skidding to safety.
The game burst into life in the 30th minute when Conor Newton, impressive throughout in the Saints midfield, galloped towards the Motherwell box.
Keith Lasley stretched out a leg, bringing Newton to the ground, with referee Thomson immediately pointing to the penalty spot.
However, after strong protests from the visitors and a brief chat with the nearside assistant referee, the decision was reversed and a free-kick awarded on the edge of the box.
Danny Grainger blasted the resultant set-piece high and wide.
Interview - Motherwell manager Stuart McCall
It was somewhat ironic, then, that St Mirren were a goal down eight minutes later.
Zaine Francis-Angol pinged an angled cross towards John Sutton and his header from 10 yards squirmed through the legs of Cornell in the Saints goal.
Motherwell displayed more composure on the ball after the half-time interval and began creating opportunities to extend their lead.
Shaun Huthinson smacked the bar with an unopposed header from an Iain Vigurs corner.
Then Henri Anier squandered an opportunity to make it 2-0 when one-on-one with Cornell.
The introduction of Kenny McLean and Thomas Reilly injected some energy into the home side and, in the dying moments, a skirmish in the Motherwell six-yard box had the home fans on their feet.
However, the ball did not drop kindly to a black and white shirt and the Steelman held on to claim all three points.
St Mirren 01 Cornell 04 McGregor 06 Goodwin Booked 14 McAusland 27 Grainger (Caprice - 72' ) 08 Harkins (McLean - 81' ) 10 McGowan 21 Teale 24 Newton 09 Thompson 19 Bahoken (Reilly - 68' Booked ) Substitutes 30 Dilo 02 van Zanten 05 Mair 07 McGinn 11 McLean 16 Caprice 17 Reilly Motherwell 01 Hollis 03 Hammell 05 Hutchinson Booked 06 McManus 17 Francis-Angol (Cummins - 86' ) 07 McFadden (Lawson - 75' ) 11 Vigurs 14 Lasley 18 Carswell 09 Sutton 24 Anier (McHugh - 68' ) Substitutes 12 Nielsen 15 Cummins 08 Lawson 25 Ainsworth 26 Leitch 16 McHugh 22 Moore
Ref: Craig Thomson