Fowler once again put himself in contention for a first major title at Valhalla on Sunday, but had to settle for a share of third as McIlroy ultimately prevailed to claim his third title in a row following previous successes at The Open Championship and WGC-Bridgestone Invitational.
McIlroy reclaimed top spot in the Official World Golf Ranking with the second of those victories, and now boasts four major wins at the age of 25.
A gracious Fowler, also 25 and runner-up to McIlroy at The Open together with Sergio Garcia, acknowledged the stunning form of his rival.
"Obviously, Rory played great this week, and he's been a deserving champion the last three tournaments," said the American, who finished two behind the champion at 14 under and one adrift of playing partner Phil Mickelson.
"He's playing quite good right now. Best player in the world, hands down.
"We'll see if we can sneak one [major] away from him at some point."
The consistent Fowler put himself in esteemed company in Kentucky, becoming only the third player to secure top-five finishes at all four majors in the same year.
Only Jack Nicklaus and Tiger Woods have previously achieved such a feat, and Fowler took to Twitter to express pride in his efforts.
"Looking back...petty [sic] cool to join @TigerWoods and @jacknicklaus as the only three to have finished top 5 in all 4 majors in the same year," he wrote.
Reflecting on coming close to glory once again, only to be denied, Fowler had earlier told reporters: "I really felt like I could win this one."
He continued: "I'll be able to look back and learn a lot from the majors this year."