Two-time major champion Kaymer carded a 69 on Saturday to make up his one-stroke deficit on the Spaniard, who has led since the opening day.
"Mentally I'm really excited about tomorrow," Kaymer said. "It doesn't really matter what happens tomorrow, if you win or not, it's nice to be in that position to have an opportunity to win a golf tournament."
Kaymer has been after his 12th tour title since winning the U.S. Open seven years ago.
Canizares won the last of his two titles at the Trophée Hassan II in Morocco in 2014 and had to fight his way through the last two qualifying schools.
The Spaniard carded two double-bogeys on Saturday, on the par-four seventh and 10th, but won four straight strokes from Nos. 3-6. Kaymer dropped two strokes on the back nine and had five birdies.
Nicolai von Dellingshausen had eight birdies and dropped just one stroke for a 65, the best round of the tournament so far. The German climbed to eighth, four strokes off the lead.
The event at the Diamond Country club, near Vienna, is the first European Tour event in 2021 taking place on the continent.