The visitors were quickest off the starting blocks, with Jonas Hoffman attempting a snapshot from range after two minutes played, but the ball sailed over the bar.
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Sven Bender was next to threaten in the 12th minute, leaping high to connect with a corner, but again the effort was just off target.
It was all Dortmund in the early stages of the game, and Gonzalo Castro came close to putting his side in the lead when he was played clean through on goal in the 24th minute, but Robin Olsen was able to thwart his attempt.
Despite this, the first goal came the way of the hosts in the 34th minute, as Robert Mak was played into space courtesy of an incisive through-ball before unleashing a ferocious shot that rattled off the crossbar and into the net.
It proved more of the same after the restart, with Thomas Tuchel's charges dominating proceedings on the pitch but PAOK nearly striking again, though Garry Rodrigues's 25-yard effort sailed wide of the left post.
Dortmund's endeavours would not go unrewarded, however, as Castro succeeded in finally getting his side back level in the 73rd minute thanks to a deadly curling effort from long range which left Robin Olsen scrambling at thin air.
The Greek outfit came close to retaking the lead nine minutes from time, with Jairo played in on goal and allowed to pull the trigger from close range, but Roman Weidenfeller was able to thwart the young Brazilian's strike.
Dortmund climb to the top of Group C following their point, while PAOK edge up to third.