Fraser Wright struck twice as Kilmarnock reached their first semi-final since 2001 in a lively CIS Insurance Cup clash at Rugby Park.
Wright put Killie ahead at the start and end of the first half and gave away a penalty that Richie Foran converted in between.
David Clarkson's equaliser as Killie's Peter Leven lay injured sparked a touchline confrontation that saw Well boss Maurice Malpas sent off before Danny Invincibile curled home a superb winner.
Both sides made one change at left-back with Garry Hay returning from injury for Killie to replace Ryan O'Leary and Marc Fitzpatrick stepping in for the injured Jim Paterson.
The visitors began well but in the seventh minute they conceded a carbon copy of the soft goal that lost them last season's semi-final against Celtic, although the players involved were different.
Fitzpatrick
casually passed the ball back without realising
Colin Meldrum had rushed to the edge of his box and
the Well keeper had to pick it up.
The free-kick was rolled to Fraser Wright - the match-winner in the previous round - who lashed it into the bottom corner from 12 yards.
Calum Elliot soon had a great chance to level when he latched on to a long clearance to go through on goal but Graeme Smith blocked and Clarkson could not follow up.
Well were passing the ball around impressively when they went forward and Elliot's shot took a deflection and looped just over the bar.
Killie came close to a second when Colin Nish looped a header on to the bar after an Allan Johnston cross.
Wright went from hero to villain when he brought Clarkson down after letting the Well striker sneak in front of him while attempting to shepherd the ball back. Foran drove the 25th-minute penalty into the bottom corner.
Killie almost regained the lead instantly when Steven Naismith rolled in Invincibile but the Australian drove the ball past the far post.
Meldrum then smothered Nish's 25-yard drive, which bounced off the wet surface just in front of him.
But
Fraser Wright headed Killie back in
front on the stroke of half-time when he beat the
former Killie keeper to Leven's long free-kick and
headed home from six yards.
Well survived another scare after the restart when Meldrum smothered at the second attempt as Craigan tried to shield the ball from Naismith.
Nish should have added to the lead when Leven's cross found him unmarked six yards out but the ball hit off him and fell for Meldrum.
And Motherwell scored a controversial equaliser in the 59th minute as Leven lay prostrate inside his own half after Brian Kerr had won a 50-50.
Well had every right to play on but as the Killie fans called for the visitors to put the ball out Steven McGarry floated the ball to the back post and Clarkson slipped the ball under Smith.
Wright was booked for dissent in the aftermath before Malpas was sent from the dugout after a clash with opposite number Jim Jefferies.
Well had the momentum and Gordon Greer did well to divert Elliot's shot.
But
Danny Invincibile put Killie back in
front in the 71st minute when he collected a Gary
Wales lay-off and curled a left-foot shot into the
top corner from 20 yards despite Meldrum getting a
hand to it.
Sub Wales stabbed the ball a foot wide after running on to Greer's headed clearance before colliding with the onrushing Meldrum, but ref Kenny Clark gave a goal-kick.
The Well keeper enjoyed some good fortune when he blocked Naismith's shot with his feet after Paul Quinn had missed a long ball.
The visitors were struggling to mount any attacks and Nish shot weakly at goal after Grant Murray's cutback.
Wales - just back from knee surgery - was replaced as the 90 minutes drew to a close.
And Mark Reynolds hooked Well's last chance over the bar after a free-kick into the box had caused chaos.
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