McIlroy finished third along with six other players at the Kasumigaseki Country Club.
But in the seven-man play-off for a bronze medal McIlroy’s hopes disappeared when he missed a birdie putt at the third extra hole.
Chinese Taipei’s CT Pan eventually beat Open champion Collin Morikawa at the next hole, to finish outright third behind gold medallist American Xander Schauffele, and Slovakia’s Rory Sabbatini.
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McIlroy was disappointed to miss out on a medal but admitted his experience in Tokyo had changed his opinion on golf in the Olympics.
“I made some comments before that were probably uneducated and impulsive, but coming here experiencing it, seeing, feeling everything that goes on, not just Olympic golf but just the Olympics in general, that sort of Olympic spirit’s definitely bitten me,” McIlroy said.
“It makes me even more determined going to Paris and trying to pick one (a medal) up. It’s disappointing going away from here without any hardware, I’ve been saying all day I never tried so hard in my life to finish third.
“But it’s been a great experience. Today was a great day to be up there in contention for a medal, certainly had a different feeling to it than I expected and I’m already looking forward to three years’ time and trying to go at least one better, but hopefully three better.”
McIlroy opted not to compete in the golf event at the 2016 Rio Games, and decided to represent Ireland despite being born in Holywood, Co Down and eligible to play for the Great Britain team.
In an interview with the Mail Online in 2012 he tried to explain his dilemma over Olympics representation.
“What makes it such an awful position to be in is I have grown up my whole life playing for Ireland under the Golfing Union of Ireland umbrella,” McIlroy said.
“But the fact is, I’ve always felt more British than Irish.
“Maybe it was the way I was brought up, I don’t know, but I have always felt more of a connection with the UK than with Ireland. And so I have to weigh that up against the fact that I’ve always played for Ireland and so it is tough.
“Whatever I do, I know my decision is going to upset some people but I just hope the vast majority will understand.”
McIlroy’s Irish teammate at Tokyo Shane Lowry finished tied 22nd.
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