The 21-year-old German had just put in arguably the finest performance of his fledgling career in knocking out 20-time grand slam winner Federer in the semi-final.
But an incident in the second-set tie-break completely overshadowed his 7-5 7-6 (5) victory.
When a ball boy dropped a ball during a rally, behind Federer but in Zverev's sight line, the German motioned to halt the rally.
A contingent of Federer fans were unhappy that the umpire - in accordance with the rules - agreed to replay the point, particularly when a subsequent ace flew past their idol.
Federer later insisted he did not call Zverev's sportsmanship into question, although he did say his opponent's decision to stop mid-rally was "a bold move".
At the concusion of the match Zverev was jeered as on-court interviewer Annabel Croft began to speak to him, with Croft at one point admonishing the crowd for their reaction.
A clearly upset Zverev told Croft: "I'm very sorry that this happened. I didn't mean to upset anybody - that's all I can say. Sorry."
BBC presenter Sue Barker said she felt "quite embarrassed that a British crowd could put him through that".
Pundit Tim Henman added: "He's done absolutely nothing wrong. Once Federer understood the situation he totally accepted it. To be booing a young, talented guy like that is disappointing."
Afterwards Federer said: "I understand the (crowd's) frustration. It's just unfortunate circumstances. These things happen.
"Booing, I never like it. We see it in other sports all the time, but in tennis it's rare. So when it happens, it gets very personal and we take it very direct.
"He doesn't deserve it. He apologised to me at the net. I was like 'you don't need to apologise to me here'."
As for the unfortunate ball boy, Federer added: "It's all good. I hope he doesn't have a sleepless night. It's not a big deal at the end of the day.
"Whatever happened, this is life, this is sport. I'm definitely not mad at him."
The jeering marred what had been a high-class encounter, miles above anything else witnessed during a distinctly humdrum week by the Thames.
A nip-and-tuck first set was taken by Zverev when he broke Federer to love at 6-5.
The youngster, yet to make it past the quarter-finals of a grand slam, showed no signs of nerves in a pulsating second set to send Federer spinning out of his 15th semi-final in 16 appearances at the tournament and prolong his wait for a 100th career title.
Earlier, Britain's Jamie Murray and Brazilian Bruno Soares lost their doubles semi-final 6-3 4-6 10-4 to Americans Mike Bryan and Jack Sock.
