The Dutchman, who took his Bundesliga tally to 16 goals, 14 of which have come since the start of the year, tapped in twice at the far post after Timm Klose's header gave the visitors the lead as they ended a three-game league run without a win.
Paderborn, in 17th place, scored a late goal through Lukas Rupp's powerful shot.
Wolfsburg, who last played in Europe's premier club competition after winning the 2009 Bundesliga title, can also clinch the German Cup when they take on Borussia Dortmund in the final later this month.
"Huge congratulations to my team for taking the decisive last step," coach Dieter Hecking told reporters. "In the last three games we dropped too many points and that was unnecessary.
"We look forward to the last two games of the season as we really want to defend second place."
The Wolves are second on 65 points, two ahead of Borussia Moenchengladbach, and seven ahead of fourth-placed Bayer Leverkusen.
Schalke 04's slump continued with a 2-0 loss at Cologne, who are guaranteed another season in the Bundesliga.
The Royal Blues, however, have one win from their last eight games with their Europa League hopes dented after they dropped to sixth place on 45, only two behind Borussia Dortmund and Werder Bremen.
Bayern Munich, who have already secured the title, lost 1-0 to Augsburg on Saturday for their fourth defeat in a row in all competitions.
Pep Guardiola's team host Barcelona in their Champions League semi-final second leg on Tuesday, trailing 3-0.
(Reporting by Karolos Grohmann; editing by Toby Davis/Mark Meadows)
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