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 29-year-old helped make his name in a 2-1 victory over Celtic in September 2002 when he scored and tormented Martin O'Neill's side.
His lack of game time meant he was never going to be running at Celtic in the same way this time but his skill, improved football brain and willingness to work helped Motherwell boost their hopes of qualifying for Europe.
It was Nicky Law who proved the key player though as the midfielder's forward runs and composure set up both goals.
Inverness dropped a place to third and Dundee United moved up to eighth after a goalless draw.
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.
Motherwell leapfrogged the Highlanders with their 2-1 win at home to leaders Celtic, while United moved above Aberdeen to within one point of the top six.
Hibernian twice came from behind to earn a 2-2 draw in their contest with Kilmarnock - with three of the goals coming in a lively finish.
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.
Graham Carey scored a goal of the season contender as St Mirren defeated Hearts 2-0 in their match at St Mirren Park.
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.
Mark Stewart got new interim Dundee boss John Brown off the hook in his first game in charge as he bagged a late equaliser in a 2-2 draw against St Johnstone.
Steven 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 Declan Gallacher's dismissal following his last-man tug on .MacLean. However, just as the visitors thought they had done enough for the Tayside derby win, Stewart struck at the death.