Zverev's previous loss to Sinner came 11 days ago, going down 6-0, 6-1 at the Paris Masters, but in Turin the two-times winner of the season-ending championships had the majority of break points, but unlike the Italian, he failed to take advantage.
Sinner forced break points in one game in each set, enough to claim victory and a place in the semi-finals, while Zverev had seven across four games.
In the Vienna Open final 17 days ago, Zverev managed to win one set, but this time around the German could not find a way past Sinner's serve.
"I think generally today, the biggest difference was how he was serving on the break points," Zverev said.
"I had more break points than him. I felt very good from the baseline, actually better than in Vienna almost, when we were in the rally.
"To be honest, he had two chances to break me, and he used both of them. I had a lot of chances, and I didn't use any."
Sinner hit 12 aces, many of which came at crucial points. In the opening game, the Italian served up four aces alone, two of which saved break points, and came from 0-40 down early in the second set with an ace winning that game.
"Sometimes when he's serving like this, it's even more difficult because, seven break points, seven first serves, not one second serve I had," Zverev said.
"I was not even in the rally at all. I think I made one return. He hit a forehand winner.
"He improved his serve a lot. All in all, from the baseline, how the game was, I thought it was a good match, which maybe was closer than the score says."
Zverev was asked if Sinner's performance was unplayable.
"It's not unplayable. I had many opportunities. He had one, he used the chance," Zverev replied.
"Of course I think it's quite easy for you guys to ask these questions because the score says 6-4, 6-3. If you look deeper into the match, I really believe that it could have been better than 6-4, 6-3.
"So... don't always judge it by the score."
Zverev won his opening match against Ben Shelton, and a win over Felix Auger-Aliassime on Friday would see him advance to the semi-finals from the Bjorn Borg Group, and he could meet defending champion Sinner again in the decider.
"Listen, I hope to see him again, it's as simple as that, this week," Zverev said.