Centre Court witnessed one of the greatest upsets of all time on Wednesday evening as Federer lost 6-7 (5/7) 7-6 (7/5) 7-5 7-6 (7/5) to the unseeded Ukrainian, who has only made the second round at SW19 once before and is currently ranked 116th in the world.
The defeat brought to an end Federer's incredible run of 36 consecutive appearances in grand slam quarter-finals.
Last year the Swiss upset the odds to equal Pete Sampras' record of seven titles at the All England Club.
Given that he will be 32 the next time the championships come around, many have already started speculating that Federer has past his best, but the 17-time major winner laughed off such talk on Wednesday night.
When asked whether it felt like the end of an era, Federer bluntly replied: "No. I still have plans to play for many more years to come.
"It's normal for people to feel different after losing early all of a sudden.
"I'll be okay. I'm very happy about it. I wish [my run] wasn't going to end here today [Wednesday].
"But I don't think that's something fans are going to mourn, and neither am I.
"I can't panic at this point, that's clear. I just have to go back to work and come back stronger really.
"It's hard to do sometimes, but usually I do turnarounds pretty good.
"There's still a lot of tennis left.
"I'll appreciate what I've achieved when I'm retired and that's not right now."
Speculation about Federer's glorious career being on the wane is nothing new.
The Swiss went through a barren patch of nine failures in majors as Novak Djokovic and Rafael Nadal asserted their dominance on the men's game, but the 31-year-old came back to last summer to win at the All England Club.
On Wednesday he had no answer to Stakhovsky's serve and volley tactics on Centre Court.
Asked how he might reflect on his victory in his old age, the Ukrainian said with a smile: "I can definitely tell my grandkids: 'I kicked the butt of Roger Federer'."
Federer strutted confidently on to Centre Court, this time not wearing the outlawed orange-soled trainers he wore in the first round, and edged a tight first-set tie-break.
Stakhovsky failed to take two break points in the second set, but he then nicked a tie-break to level the match.
Stakhovsky broke again in the third set after Federer ploughed in to the net from the baseline and the Ukrainian's historic victory was sealed after a tense third tie-break of the match.
"Beating Roger here on his court, where he's a legend, is I think having definitely a special place in my career," said Stakhovsky, who will now play Jurgen Melzer in the third round.
"Roger Federer is the greatest player we had. He's the biggest name we had and we still have.
"I think as a person he showed us that you don't have to be really somewhere else, you can be a decent man achieving a lot of things and still be a person which everybody admires."
Part of the reason behind Federer's success over his glittering career has been his ability to bounce back while under pressure.
Yet he was unable to pick himself off the canvas and comeback against Jo-Wilfried Tsonga at the French Open last month, when he lost in straight sets to the home favourite, and he was clearly annoyed at being unable to launch a fight back against Stakhovsky on Wednesday night.
"I'm very disappointed about that I couldn't find a way, like against (Tsonga) at the French Open," Federer said.
"I had my opportunities, but when I had the chance, I couldn't do it.
"It's very frustrating, very disappointing."
Federer was at a loss to explain why he was unable to beat his opponent.
He added: "I didn't feel any different today [Wednesday], like I felt something was coming.
"Today [Wednesday] was a normal day. I had a normal warm-up, it was a normal match really.
"I was hoping to win the match today [Wednesday], but I couldn't do it so it's clearly disappointing."