The Scottish giant started much the brighter of the two teams, but the hosts grew into the game and went ahead after 27 minutes, when a powerful drive from captain Teddy Teuma was too hot to handle for Jon McLaughlin.
In the Belgian side's first ever Champions League appearance, they were awarded a controversial penalty with 17 minutes remaining after a Teuma shot ricocheted off Ben Davies onto Connor Goldson's arm.
After a lengthy VAR check, Dante Vanzeir stepped up and calmly sent McLaughlin the wrong way as he rolled the ball into the bottom-right corner.
The hosts nearly added a third goal late on, but Rangers captain James Tavernier blocked a Christian Burgess header off the line in the dying seconds.
The outcome means Giovanni van Bronckhorst's Rangers will have to be at their best in the return leg at Ibrox next Tuesday to overturn the two-goal deficit.
They are looking to take a step towards reaching the Champions League group stage for the first time since the 2010-11 season, with the winner of this tie going into a play-off against PSV or Monaco.