Federer secured his place in the semi-finals of the ATP World Tour Finals for a record 14th time with a three-set win over Zverev, a debutant at this tournament.
The 20-year-old fought back from a set and a break down to force a deciding set but went to pieces and won just one game in the third.
And the German admitted that he had used the slice backhand to great effect to disrupt his efforts.
“He’s the best player of all-time,” Zverev said.
“He’s always going to find a way to try to disturb your rhythm a little bit and try to win.”
He added: “I think people have realised that if you go fast to my backhand with a lot of spin, I quite like it.
“So maybe people are starting to change it up, go a little bit more with the slice.”
But Zverev bemoaned his own inability to retain his composure after losing his serve in the early stages of third set.
“I think he played a very good game to break me,” Zverev said.
“Then I lost a little bit concentration after that.
“But, look, all in one, I think it was a very positive match. Obviously he won it.
“He’s in the semifinals. But even for me, I played the better match of the two today.
“I think I still have great chances of qualifying, playing Jack Sock next.
“I think if I continue having this level, I don’t know, maybe you’ll see me on the weekend still.”