McIlroy, ranked No. 1 in the world and a four-time major winner, was seemingly out of contention when he began the final round at Chambers Bay, eight strokes off the pace of four co-leaders.
But three birdies on the first nine followed by three in the first four holes on the second side had him 6-under par for his round and thinking about matching the major championship record of 63 or even becoming the first to ever shoot 62.
The biggest final-round comeback at the U.S. Open was 7 strokes by Arnold Palmer in 1960.
McIlroy went the other way, however, settling for a 4-under-par 66 after two bogeys coming in and finished the tournament at even par 280.
"When I look back, obviously the last few holes of this golf course haven't been kind to me all week,'' said McIlroy, who played holes 14 through 18 in 6-over par for the tournament. "And when I look back at this tournament that's where I'll rue some missed opportunities.
"I feel like it's sort of one that got away, especially the way I putted this week. I don't think I've ever hit the ball as well in a major championship.''
That's saying something considering McIlroy won two of his four majors by eight strokes and had that strong run last summer at the Open Championship and PGA Championship.
But McIlroy had gotten to 2-under par for the tournament and within striking distance of the leaders after holing an improbable 70-foot birdie putt at the 13th. He had two good birdie holes remaining in 16 and 18 to get to 4 under -- which would have meant a 62 for the round on the par-70 course.
There have been 26 scores of 63 in major championships, including one by McIlroy in 2010 at the Old Course at St. Andrews. But no one has ever shot 62.
Johnny Miller in the 1973 U.S. Open at Oakmont is the only player to shoot 63 on the final day and win. At the 14th, McIlroy missed a good birdie opportunity inside 10 feet, and then followed with a bogey at the par-3 15th when his tee shot hit near the pin but rolled off the green.
"I don't think it derailed the momentum,'' McIlroy said. "It would be nice to have holed it. I felt like I hit a good putt for once that didn't go in. Then the missed putt on 15, for the first bogey of the day, that hurt. And not to birdie 16 from where I put it off the tee. And then again a three-putt on 17.''
A double bogey-bogey finish on Friday also had McIlroy kicking himself, those three shots big on a day when trying to make up so much ground proved to be too big of a challenge.
Now McIlroy heads to his home in Florida for a few days before going to Europe. He'll spent time in Northern Ireland, perhaps get in some practice at St. Andrews, then head to the Scottish Open the week prior to the Open Championship.
"This bodes well for the rest of the summer the way I've hit the ball this week,'' he said. "And I've got a couple of weeks to work on my putting and get that up to the shape that it has been in and especially the way it was last year. If I can do that, keep the long game where it is, I'm really excited about what can happen over the summer.
"I take a lot of positives out of this. The long game is really in good shape. I've never hit the ball as good in a major championship for four rounds. I was really dialed in all week and confident with that. And if I can just get the putting a little bit better and roll a few more in and get a little bit of confidence with that going, I see nothing but positive signs for the next few months.''
Spieth wins U.S. Open
SportsCenter Highlight of the Night: Jordan Spieth wins the 2015 U.S. Open at Chambers Bay by 1 shot after Dustin Johnson three-putts on the 18th hole.