The defender, who was with Zwolle between 2007 and 2011, thumped home a header 20 minutes from time to boost Groningen's UEFA Europa League hopes and simultaneously damage those of their opponents.
Groningen came into the game in eighth place, a point ahead of their rivals in the race for a Europa League play-off berth, and now boast a four-point cushion with just three league games remaining.
Ron Jans' Zwolle entered the clash with just one win in their past eight league outings, and their struggles continued as the hosts struggled to create any clear-cut chances.
After a turgid first half, Zwolle's Fredua Benson saw his near-post effort beaten away by Marco Bizot, before Richairo Zivkovic fired off-target when well-placed for the visitors.
Three minutes later, however, Groningen were in front, Botteghin left all alone at the back post to power home Maikel Kieftenbeld's deep cross from the right.
Bizot was called into action once more in the closing stages, denying Bart van Hintum at the front post as Erwin van de Looi's men held out to put secure their third successive league win.
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