They moved on to 17 points, one behind Werder Bremen, while Fortuna remains third from the bottom with 23 as they were left on a sunny afternoon at the Dusseldorf Arena to rue some poor fortune.
Fortuna's Valon Berisha struck the woodwork twice as he continued his quest for a first goal for his new club since moving from Lazio on loan in January.
Team mate Steven Skrzybski has also been unfortunate in the last 10 minutes to see his strike cannon back off the post.
Paderborn might have snatched a three-minute unlikely win from time to time, but Nigerian international Jamilu Collins squandered a good chance from close up.
Fortuna had the game's first real chance in the 14th minute, when the ball was passed across the forward line before the subsequent shot of Matthias Zimmermann was blocked.
Berisha came within inches of his first goal three minutes later as his volleyed effort took a deflection off defender Sebastian Schonlau and struck the upright only to bounce back into play.
A defensive error presented Mohamed Drager of Paderborn with a half chance on the half hour but he was quickly shut down, only for Fortuna to then threaten on the other end as Kaan Ayhan's header from a freekick went narrowly wide back center.
It took the second half a while to generate any flow before Fortuna winger Erik Thommy started taking a grip on the game, setting up several opportunities.
Before Berisha powered a header from close range in the 66th minute against the crossbar he was involved in the build-up.
Substitute Skrzybski then thunders his shot at the left post to add frustration to the home side.
But after missing a chance against the play run as full time approached, Collins will have some explanation to do to his Paderborn team mates. Had he scored, only their fifth win of the league campaign could have given Paderborn.
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