Rather than wait to see where the ball might end up, Mickelson literally ran after the ball and hit it again as it was still moving.
That was a 2-stroke penalty and Mickelson ended up with a 9 on the hole. The 10 was the highest score on any hole at this U.S. Open, according to the USGA.
He himself apologised, insisting that he had "meant no disrespect".
"I think he just snapped".
Strangely, the USGA deemed that Mickelson "played" the moving ball, rather than "moving or stopping" it, which could have brought disqualification into play. "I don't know if I would have been able to save a shot or whatnot, but I know it's a two-shot penalty hitting a moving ball, I tried to hit it as close to the hole as I could to make the next one. It was unusual, no one ever has those thoughts, it just happens". He hustled after the putt - and hit it back toward the hole before it stopped rolling.
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It was not immediately clear what was Mickelson's motive in striking the ball.
The most recent time something like this happened at a major tournament was John Daly at the 1999 U.S. Open at Pinehurst, when he hit a moving ball on the green en route to an 83 and a dead-last finish.
RTÉ golf correspondent Greg Allen said the incident is causing a lot of bemusement among the media and galleries at Shinnecock Hills.
Either way, it's a remarkable turnaround from Mickelson's optimism from earlier in the week, when he was hoping to complete the career Grand Slam.
Mickelson, who has been a US Open runner-up six times, most recently in 2013, was having a miserable time Saturday before reaching 13. He now sits 17-over for the championship.