Eoin Doyle headed the hosts ahead five minutes before half-time and doubled his tally nine minutes after the break when he raced onto Paul Cairney's high ball and his strike rocketed past Darren Randolph.
Jamie Murphy tapped in from close range to cut the hosts' lead and he glanced home a leveller with 10 minutes remaining.
Hibs looked shell-shocked after losing a commanding lead and things got worse for Pat Fenlon's side when substitute Robert McHugh converted Henrik Ojamaa's cross two minutes from time.
James McPake was dismissed for a second yellow card during injury time to complete a miserable afternoon for Hibs, who now trail Motherwell by three points in the Clydesdale Bank Premier League table.
"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 - there were a few choice words at half-time," said McCall.
"I challenged our lads to match their spirit and I felt the game wasn't over at 2-0, we showed the commitment and desire to go on and win the game. 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 (they were defeated by Aberdeen in the William Hill Scottish Cup), ourselves included, but we are doing fantastically well in the league."
McCall was also delighted at the impact of substitute McHugh, who passed up a glorious opportunity before grabbing the winner.
"I'm not sure what happened with the first chance and a few of the lads are giving him a bit of stick in the dressing-room - I thought he had a tenner on 2-2," joked McCall. "I was delighted for him and hopefully he can continue to come on and nick a few goals."
- Sports & Recreation