The German world number seven claimed his third ATP Tour win on home soil as third seed Auger-Aliassime lost his sixth successive final.
Albot, who also struggled when receiving with a 32-per-cent conversion rate on return points, was successful on his only break opportunity of the match.
"In my mind I knew it was goint to be a hard match", said Auger-Aliassime. "As a player you know you're happy when your shots are going where you want them to go, and that's really how I felt today". Bautista Agut prevailed over 2 1/2 hours to beat Hubert Hurkacz 7-6 (4), 5-7, 6-0.
Zverev has already qualified for the season-ending ATP Finals in London next month but will remain in Cologne for the bett1HULKS Championships next week where he is again the top seed.
"He played much better tennis and I think he's somebody who is going to go up the [FedEx ATP] Rankings very quickly", Zverev said.
"This is our first final, but probably not the last", said the 21-year-old Canadian after he defeated the Spaniard, 6-3, 1-6, 6-3, to reach his third final of the year.
Davidovich Fokina would save the breakpoint with an incredible volley victor but the number one seed would not be denied and broke at the third time of asking to take a 3-1 lead.
The seventh-ranked Zverev next faces Alejandro Davidovich Fokina. Alexander defeated Felix twice in 2019 and is still flawless against the 20-year-old, dropping only 12 points in nine service games today to give serve away only once.
Bautista Agut is playing his second semifinals of the season after reaching the last four in Cincinnati, where he fell to Novak Djokovic.
- With files from The Associated Press.