McIlroy's playing competitor Kyle Reifers, who was standing next to the Northern Irishman, raised his hands angrily after the near miss.
McIlroy, who shrugged off the incident to drain a 10-footer to save par, later absolved Grillo of any blame.
"Missed me by a couple inches. Would've put me out of my misery, to be honest with you," he told reporters after another frustrating day on the greens.
"I mean, they obviously thought the green was clear. Not his fault. You can't see much from back there."
Golf Channel commentator Peter Jacobsen was not so forgiving.
"I just can't imagine what Grillo was thinking back there on the tee," Jacobsen said.
Grillo told Golf Channel that no officials had been on the tee at the 296-yard hole, which requires a blind drive, and that his threesome had made a group decision to hit. The green is blocked from view from the tee by a clump of pine trees.
Four-times major champion McIlroy returned to action just two months ago after missing the British Open with a ruptured left ankle ligament he suffered playing soccer.
He shot a second consecutive 71 on Saturday to slide out of contention at the Silverado Resort in Napa in the opening event of the 2015-16 PGA Tour season.
McIlroy trails leader Brendan Steele by eight shots.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Larry Fine/Peter Rutherford)
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