The 35-year-old from Northern Ireland, who finished the day two shots adrift of leader Russell Henley, aced the par-three 15th hole at Spyglass Hill after lofting a wedge 119 yards off the tee and directly into the hole.
“Honestly, it was lucky, I don’t see many balls nowadays go straight in the hole and stay in the hole,” McIlroy said afterwards.
“Pretty fortunate because it could have come out and went back in the water or do anything. It was a good swing, good wedge shot.”
McIlroy’s hole-in-one was the highlight of a bogey-free round that also included four birdies and 13 pars.
It was one of two aces recorded by Irishmen during Thursday’s opening round, which was held over two separate courses in northern California at Spyglass Hill and the Pebble Beach Golf Links.
Former British Open champion Shane Lowry emulated McIlroy, acing the 113-yard par-three seventh hole on the Pebble Beach layout.
Lowry also carded a six-under-par round, making five birdies and a bogey for a 66.
McIlroy and Lowry were tied for eighth along with five other players on six under.
World number one Scottie Scheffler, meanwhile, was one shot back on five under after an opening 67.
Scheffler, playing in his first tournament since injuring his hand in a freak Christmas dinner accident last month, started slowly with a bogey on the first at Spyglass Hill.
He was soon in the groove, though, with two birdies before the turn and four more down the stretch to finish the day three off the lead.
Scheffler’s American compatriot Henley, meanwhile, took sole possession of the first round lead with a sizzling eight-under-par 64 at Spyglass Hill.
Henley reached the turn at four under after making four birdies on a bogey-free front nine, and then dropped to seven under with birdies on the 10th, 11th and 13th holes.
A bogey on the 14th checked his momentum but a birdie-birdie finish on the 17th and 18th holes left him sitting on a slender one-shot lead.
“Nice way to finish and definitely excited about how I’m playing,” Henley said.
“I feel like today the course was gettable … it was a little less windy and rainy than I’ve played in years past,” he added. “I was reading the greens well and hitting my lines.”
A low-scoring opening round left a slew of players within striking distance heading into Friday’s second round.
Austria’s in-form Sepp Straka — coming off a victory at the American Express in Palm Springs two weeks ago — is one of six players tied for second place after shooting a seven-under-par 65 which featured eight birdies.
That chasing pack also includes England’s Justin Rose, whose 65 on the Pebble Beach course included four birdies in his final three holes to move him up the leaderboard.
Rose sealed his round by rolling in a 25-foot birdie putt on the par-four 18th. Other players tied for second include Norway’s Viktor Hovland and Denmark’s Rasmus Hojgaard.
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