Eoin Doyle's brace inside the hour had put the hosts in control, before Jamie Murphy netted two of own to level matters 10 minutes from time.
Robert McHugh fired Motherwell's winning goal with 87 minutes on the clock before Hibs lost James McPake during injury time after collecting a second yellow card.
Manager McCall said: "It was a very satisfying victory. I don't know if it was a little hangover from the cup but, in the first half, we never got going and there were a few choice words at half-time.
"I challenged our lads to match their spirit and I felt the game wasn't over at two-nil either.
"I made a few changes, sometimes they work and sometimes they don't.
"I think you could see from the reaction of the lads after we got the second goal that we wanted to go on and grab a winner.
"We let a lot of people down on Tuesday night in the Scottish Cup but we are doing fantastically well in the league."