The visitors nearly went ahead when Jordi Gomez struck the post from a free kick in the 35th minute, but they still managed to take the lead just before half time.
Nick Powell was brought down inside the area, giving Gomez the chance to step up from 12 yards - although he was perhaps fortunate to see it squirm underneath the goalkeeper on its way into the net.
However, Maribor were awarded a penalty of their own moments later when Chris McCann handled in the box, thus receiving a second yellow card.
Dejan Mezga did the honours, levelling things up before half time.
The home side went ahead courtesy of a stunning 59th-minute strike from Zeljko Filipovic, but the teams were evened 15 minutes from time when Ales Mertelj was shown a second yellow for a reckless challenge on Jordi Gomez.
There was to be no fairytale comeback for Uwe Rosler's men, though, as they exit the competition despite Zulte Waregem losing at Rubin Kazan.