With just one stroke separating Johnson from Shane Lowry atop the leaderboard, the US Golf Association informed Johnson he could be assessed a penalty after the round for an infraction on the fifth green.
Johnson's ball moved slightly as he prepared to putt for par. He spoke with a rules official and it was determined he did not cause the ball to move so no penalty was assessed at the time.
But with the title chase at its peak, Johnson and his nearest rivals on the course were informed that USGA officials planned to review video of the incident again after his round.
But he kept his focus, and as Lowry faded with three late bogeys the entire matter became less pressing. Johnson finished with a flourish, calmly draining a nine-foot par putt at 17 and a short birdie putt at the final hole.
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"I didn't think that I did anything to cause the ball to move, but at the end of the day, it didn't affect what happened," Johnson said. "So it doesn't bother me at all."
"Some great golf by @DJohnsonPGA all week, strong way to finish overcomeing that rules farce," Tiger Woods, who missed the tournament as he continues to rehab his bad back, tweeted.
Other golfers were expressing outrage even before the round ended.
"This is ridiculous... No penalty whatsoever for DJ. Let the guy play without this crap in his head. Amateur hour from @USGA," tweeted Rory McIlroy, who missed the cut at Oakmont.
Spieth, who finished his fourth round earlier, added: "Lemme get this straight.. DJ doesn't address it. It's ruled that he didn't cause it to move. Now you tell him he may have? Now? This a joke?"
World number one Jason Day, who finished tied for eighth six shots behind Johnson, said he couldn't fault officials for informing Johnson that the penalty might be assessed.
"I'd probably rather know. I like to know where I'm at on the leaderboard."
The USGA's top rules official, Thomas Pagel, was unapologetic in the face of criticism. He said a number of factors went into the decision to dock Johnson a stroke, including the steepness of the Oakmont greens and the time that elapsed between the time Johnson put his putter behind the ball and the time the ball moved.
"We understand not everyone is going to agree with that," Pagel said.