The hosts – looking to take a place in the top flight after three seasons in the lower leagues – were expected by many to take a lead to Fir Park for Sunday’s return leg.
Instead they will go there looking to make up a deficit after goals from Lee Erwin, Stephen McManus and Lionel Ainsworth gave Ian Baraclough’s side a comfortable 3-1 win.
Darren McGregor’s late goal gives Rangers some hope of turning things around but there is no doubting the scale of the task they face in Lanarkshire at the weekend.
The success was Motherwell’s first in Govan since May 1997 and a first of any kind against the 54-times Scottish champions since December 2002.
Despite what was to unfold, Rangers began with a swagger and played with purpose as Andy Murdoch had a shot deflected behind for a corner and Marius Zaliukas headed wide.
Kenny Miller also went close with a glorious attempt, stepping away from his marker, nutmegging Keith Lasley and curling just beyond the far post from 20 yards.
It seemed a goal wasn’t far from coming as Nicky Law’s shot against his former club was beaten away well by Motherwell goalkeeper George Long.
Yet when the deadlock was finally broken after 27 minutes, it was the visitors who did it very much against the run of play.
Home ‘keeper Cammy Bell looked set to gather Erwin’s shot after he got past Zaliukas but McGregor’s desperate foot diverted it past him instead and into the net.
Having appeared so confident before, Rangers suddenly looked rattled and nervy in defence, with Lee Wallace doing just enough to deflect an Erwin header wide.
The hosts almost pulled level through Nicky Clark but Long saved superbly after initially stopping a McGregor header.
That was as close as Rangers came to ensuring they would take anything from the tie and five minutes before half-time they were two goals down.
Wallace was penalised for a foul on the touchline and when Marvin Johnson swung the resulting free kick in, former Celtic defender McManus glanced a header in.
Two minutes after the restart things went from bad to worse for Stuart McCall’s team as Motherwell went three up with a terrific counter-attacking goal.
The Ibrox side’s move upfield broke down and as Stephen Pearson burst clear, he found Erwin who teed up Ainsworth for a blistering low finish past Bell at his near post.
It took Rangers until 18 minutes from the end to create a chance of note but Long was in the right place yet again to tip substitute Kris Boyd’s strong header over.
He couldn’t keep McGregor’s strong header out though and that keeps McCall’s squad in contention, if only just.
Boyd had the ball in the net again with a minute remaining but was flagged offside so Rangers will travel in three days trailing by two goals rather than one.