And to make matters worse, manager Maurice Malpas could be without three key players for their next crucial match against St Mirren.
Leading scorer Scott McDonald and youngster Mark Reynolds will both incur suspensions following their red cads, while Jamie Paterson sustained an injury which could end his season early.
On-loan Celtic youngster Jim O'Brien gave Dunfermline the lead after just six minutes picking up a cross from Adam Hammill and sending a right-footed shot into the bottom right-hand corner of the net.
It didn't take long for the Pars to double their lead as Scott Wilson scored a rare goal - only his second of the season - as he rose above his defender to head in a Stephen Glass ball from the edge of the six-yard box.
Motherwell looked completely out of their depth with the exception of McDonald, who always provides an element of threat in front of goal.
Well's best chance came five minutes before the break when McDonald beat Dorus de Vries in the Dunfermline goal, but his angled left-foot drive went narrowly wide of the target.
Dunfermline began the second half with the same positive play and came close after less than 60 seconds of play as Graeme Smith was stretched the full extension to tip Tom McManus' free-kick over the bar.
They did extend their lead on 58 minutes when Jim McIntyre was brought down in the box by Reynolds and Glass converted the resulting penalty.
Things went from bad to worse for Reynolds when he was shown a straight red card for a deliberate handball.
But the Pars did not have a one-man advantage for long when Wilson was dismissed for a foul on Ross McCormack.
Motherwell were awarded a penalty which was converted by McDonald, but he in turn was given his marching orders less than a minute after scoring for lashing out at Scott Muirhead.
Jim Hamilton finished off Motherwell's miserable evening as he netted against his former club.