An injury-time goal from Derek Riordan gave Hibs three points but referee Charlie Richmond ruined the game.
He booked nine players – seven from Motherwell – in a baffling performance and also sent Hibs manager Tony Mowbray to the stand in the final minutes.
The home side dominated the second half and would have won by more but for Moltherwell goalkeeper Graeme Smith.
Hibs took just three minutes to get their noses in front with a brilliantly-crafted goal. Scott Brown sent Ivan Sproule scampering down the right and he cut the ball back for Steven Fletcher to apply a decisive finish.
But Motherwell came back strongly and equalised after 17 minutes. Kevin McBride's corner was headed goalwards by Jim Hamilton and, when Stephen Glass blocked the ball on the line, Scott McDonald pounced to ram the ball home.
Riordan forced the save of the match from Smith after half-an-hour as he curled a 25-yard free-kick towards the top corner of the net only to see the Motherwell 'keeper leap to his left to finger-tip the ball for a corner. The 'Well defence failed to clear Kevin Thomson's flag-kick, and the ball dropped to Gary Caldwell who looped his shot over the top.
Thomson wasted a chance himself five minutes later when, from a tight angle, he sent his shot high over the top.
Hibs should have added to their lead in the early stages of the second half. Sproule shot at the legs of Smith after being set up by Brown and, moments later, Brown set up another chance for Fletcher but his finish was tame.