The Steelmen almost got the first half off to the best possible start with David Clarkson having two great opportunities in the opening 15 minutes.
He firstly side-footed a Paul Quinn cross just over and then, at the end of a sweeping move, he tamely hit a shot at Mike Fraser from close range.
Inverness were causing problems with Don Cowie's set-pieces and Grant Munro's long throw-ins, but it took until the 40th minute before the visitors really troubled Graeme Smith in the home goal.
The first half had been evenly contested with neither keeper really being tested and at the break 0-0 was a fair reflection of the 45 minutes.
The second half got off to a poor start with neither side stringing any passes together. That was until Mark Reynolds misjudged a Ross Tokely throughball allowing Cowie in, but the midfielder chipped the ball on to the roof of the net.
Well responded well and Clarkson combined to release Keith Lasley but Fraser denied him with a fine save with his foot.
Well were next to threaten when Phil O'Donnell found Steven McGarry with a cross-field ball. The midfielder raced past Richard Hastings but hit his shot too early allowing the keeper a comfy save.
The goals finally arrived in the final ten minutes with Inverness looking to have sealed the points with ten minutes left. A Cowie free-kick floated over the Well defence for Tokely to volley past Graeme Smith from an acute angle.
Once again Well responded and were level minutes later when O'Donnell headed a McGarry cross high into the roof of the net from about eight yards out.
Then, with the game heading into stoppage time, Motherwell scored a dramatic winner.
Clarkson raced into the box and, with Munro in attendance, the Well striker tumbled and the ref immediately awarded a penalty.
Ross McCormack stepped up and confidently stroked the ball into the bottom right-hand corner as McGhee's side registered an unlikely win.