Michael Higdon volleyed the winner in the 73rd minute as Motherwell beat Celtic for the first time in exactly two years.
Chris Humphrey had opened the scoring prior to the break, before Georgios Samaras headed an equaliser for the visitors.
McFadden had come off the bench twice since re-signing for Motherwell, appearing in consecutive defeats against Dundee United and Ross County which had seen Motherwell slump from second to fourth place.
But his first start since playing for Everton against Wolves on May 6 last year saw them return to second spot.
The teams, who had shared 12 goals in their last two matches, cancelled each other out as the hosts squandered the chance to move clear in second place.
Sammy Clingan gave Kilmarnock the lead within a minute of the restart with a long-range strike, before Ryan McGivern levelled five minutes from time.
The visitors regained the lead soon after through Jude Winchester, only for Leigh Griffiths to earn Hibs a point with a third goal in as many minutes.
It was the crescendo to a scintillating second half that had nothing in common with a dull first 45 minutes.
The 10-man Dens outfit looked set for their 20th defeat of the league campaign after losing Declan Gallacher following his last-man tug on the scorer of Saint's opening goal, Steven MacLean.
But former Falkirk man Stewart popped up with a last-minute leveller to keep the basement club 15 points adrift of safety.
MacLean had headed the Perth side ahead 35 minutes in after home goalkeeper Rab Douglas sullied his 300th appearance for Dundee with a handling gaffe, but John Baird cancelled that out with his own header just before the break.
Saints struck again through skipper Dave Mackay's free-kick on 68 minutes as he made sure it was a double punishment for the hosts following Gallacher's dismissal.
However, just as the visitors thought they had done enough for the Tayside derby win, Stewart struck at the death.
The two sides will contest the Scottish Communities League Cup final next month - and Danny Lennon's side struck a psychological blow ahead of that contest with this comfortable victory.
Paul McGowan netted from the penalty spot after three minutes and Carey's impressive breakthrough extended their lead on the stroke of half-time.