Garcia said "in frustration, I damaged a couple of greens, for which I apologize for, and I have informed my fellow players it will never happen again."
It wasn't immediately clear what the extent of the damage was, and on which greens it took place.
Garcia shot a 71 and was even par — 16 shots behind Li and Johnson — at the time of his DQ.
Li, who had his own rules issues in Dubai last week when he received a two-shot penalty for having his caddie line up a putt, said he was "very, very lucky" to become the first player since Mark Pilkington (Singapore Masters, 2007) to make four eagles in one European Tour round.
He chipped in for eagle at No. 1, did the same at No. 10 from about 20 yards, and then drove to within six feet of the pin at the par-4 17th. At the par-5 18th, he holed an eagle putt from 8 feet to tie Johnson (65) at 16 under.
"Those eagles, especially the last couple shots, were really solid," Li said, "but except (from) that, honestly, my play wasn't that good."
Johnson, who had a three-stroke lead overnight, made four straight birdies from No. 9 to move to 5 under for his round. He made par in his final six holes.
"If I want to get it done tomorrow, I'm going to have to play really good golf," the No. 3-ranked Johnson said. "Haotong is a good player, and he's been playing well. So I'm looking forward to it."
On Li's round, Johnson added: "Yeah, that's pretty impressive. Four eagles in a golf tournament is pretty good, but four in one round — take that any day."
The Saudi International is new to the European Tour and is being held amid scrutiny of Saudi Arabia's human-rights record and condemnation following the killing of journalist Jamal Khashoggi.