After the first-half dismissal of skipper Stephen Craigan, Henrik Ojamaa opened the scoring on his first full start for the club before Nicky Law doubled the hosts' lead.
Andy Kirk restored hope for Dunfermline on 63 minutes, before substitute Chris Humphrey netted 10 minutes from time to secure all three points for the Fir Park side to send them into third spot.
Defeat for Dunfermline means they remain one point adrift at the foot of the SPL, although they set off with some intent, with Mark Kerr hitting wide of Darren Randolph's goal.
At the other end, the hosts were struggling to create an opening of their own until Jamie Murphy's stinging effort was well blocked by Alex Keddie.
There first real talking point came in the 18th minute, when Craigan was dismissed by referee Alan Muir following a clash with Andrew Barrowman, which also saw the Dunfermline man receive a yellow card.
Craigan appeared to move his head towards Barrowman and Muir wasted little time in flashing a red at him.
Manager Stuart McCall responded to the dismissal of his skipper by replacing Murphy with Tim Clancy as he attempted to bolster his side's defence.
From the resulting free-kick, Dunfermline came close to breaking the deadlock with Liam Buchanan forcing Randolph into a smart stop.
Ojamaa repaid McCall's decision to hand him his first ever league start when he fired Motherwell in front after 29 minutes.
The striker twisted and turned on the edge of the penalty box before striking a low shot which bounced over the outstretched arms of Iain Turner in the Dunfermline goal.
The visitors responded with a flurry of promising attacks and Joe Cardle brought out an excellent save from Randolph with his powerful close-range effort.
The Motherwell fans continued to vent their anger at referee Muir, as the whistler showed yellow cards to Clancy and then Ojamaa before the interval.
Motherwell started the second half brightly as they looked to build on their slender advantage.
Jennings flashed a shot wide of the target before the home side doubled their lead after 52 minutes.
Ojamaa got on the end of Michael Higdon's flick and he laid the ball to Law who unleashed a superb drive into the roof of the net.
In a bid to help find his side a way back into the match, visiting boss Jim McIntyre introduced Paul Willis to replace Cardle.
Willis' arrival seemed to add some extra width to the visitors' game and on 63 minutes they gave their small band of travelling supporters some hope when Kirk connected perfectly with Paddy Boyle's cross to leave Randolph with no chance.
The hosts made their second switch of the night after 71 minutes when the influential Ojamaa made way for Robert McHugh.
Dunfermline continued to probe for an equaliser and Randolph did well to hold Willis' shot from range.
Martin Hardie was introduced to replace Buchanan with 15 minutes remaining and Motherwell also made a change as Humphrey came on in place of Law.
The visitors continued their assault on the Motherwell goal and Kirk passed up a glorious opportunity to level the match on 78 minutes when he found space in the box after good work from David Graham, but his strike was inches past the post.
With 10 minutes remaining, Motherwell put the game out of the reach of their opponents, when McHugh latched on to Randolph's long ball and he found Humphrey who coolly slotted the ball past Turner.
