Juan Manuel Ortiz netted his first goal for Rangers when he fired the Glasgow giants into a first-half lead, but Agim Ibraimi levelled after the break before substitute Etien Velikonja found the back of the net in injury time.
Rangers will be bitterly disappointed that they could not hold on, but they do go back to Ibrox with an away goal in the bag.
The home side had enjoyed much of the possession without really taking advantage and they found themselves trailing when Rangers surged into the lead after 31 minutes thanks to Ortiz.
The Spaniard started the move by finding Kirk Broadfoot out on the right flank, before racing into the box where he was waiting to collect the return pass and flick home from six yards.
Maribor were back on level terms after 52 minutes when Ibraimi collected on the corner of the box from a throw-in and sent a powerful left-foot shot past Allan McGregor.
And it was Maribor who had the net bulging in injury time when Dejan Mezga teed up the shot for substitute Velikonja, who back-heeled over the line.
Rangers should have enough in them to get through the home tie, knowing that a 1-0 win would be enough to see them through to the group stages of the Europa League.
If they don't it would surely be deemed a huge failure, having failed to progress in the Champions League it is estimated that they would lose out on a staggering £18million worth of revenue.
At least getting into the group stages of the Europa League will see them gain a figure in the region of £2million. Rangers will have to up their game if they are to progress and the disappointment on the face of manager Ally McCoist was there for all to see at full-time.