Referee Craig Thomson, however, failed to produce a card after penalising Martin Canning for pushing Nick Blackman over in front of an empty goal and Motherwell's frustration was compounded when Tomas Cerny saved Tom Hateley's resulting penalty.
Hamilton battled their way through a second half of few chances to keep themselves off the bottom of the SPL.
Accies had won just one of their previous 10 matches this season but they were fresher than Motherwell, who beat Dundee United in the Co-operative Insurance Cup quarter-finals on Tuesday.
Motherwell were also missing the midfield drive of Keith Lasley, who remained sidelined by a hamstring injury, and the pace and invention of Jamie Murphy, who failed to overcome an ankle problem. Hamilton brought in defender David Elebert for midfielder Gary McDonald but their attacking 4-3-3 formation saw them start on the front foot.
Flavio Paixao curled a free-kick just beyond the far post and soon created a half-chance for Hasselbaink, who headed over from 10 yards.
Motherwell settled and Steven Saunders headed over following a Stephen Craigan free-kick but Hamilton took the lead thanks to excellent forward play from Hasselbaink. The 19-year-old took the ball in from Dougie Imrie on the edge of the box, turned his man and curled a left-footed shot in off the far post.
Hamilton grew further in confidence and Paixao saw a 30-yard free-kick held by Darren Randolph before his cutback fell kindly 12 yards out for Simon Mensing, but the home keeper held the former Motherwell midfielder's deflected drive.
Hamilton were closing Motherwell down quickly and another Paixao delivery evaded the home defence, but the untracked Jim Goodwin failed to connect properly with the back-post corner and the ball bounced over.
Motherwell missed a great chance to level from the spot in the final minute of the half.
However, Motherwell were left with a strong sense of injustice after Canning escaped further punishment for pushing Blackman over as the striker was poised to put the ball into the empty net.
Chris Humphrey had got in behind the Accies defence and cut in from the right to square the ball beyond Cerny but referee Thomson did not produce any card as the home fans shouted for a red, and Cerny dived to his right to hold Hateley's low penalty.
Motherwell pushed forwards after the break but Hamilton defended resolutely and in numbers. And, when Steve Jennings did burst through the Accies defence to allow Ross Forbes to cross just before the hour mark, Cerny produced a great diving save to stop Alan Gow's header before Imrie completed the clearance.
Saunders then headed Forbes' free-kick on to the post but the flag was raised.
Hamilton skipper Alex Neil made his first appearance since summer hip surgery when replacing Goodwin midway through the half as Accies killed the game.
Canning was eventually booked for taking out Blackman with a late and reckless challenge but Hateley's free-kick went straight into Cerny's arms.
Motherwell brought on John Sutton and Bob McHugh but Motherwell continued to be frustrated as Accies, now playing five at the back, sat in during an increasingly ill-tempered contest.
Forbes was booked for trying to haul up Paixao as the winger rolled around on the ground after being caught by the midfielder, with Neil also shown a yellow card for running to his team-mate's aid.
Mark McLaughlin was booked for a challenge more akin to a rugby tackle on Blackman in injury-time but Cerny held Hateley's low free-kick to secure the three points.
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