The world number one could have been disqualified for an illegal drop in his previous round but the Masters competition committee took a lenient approach, slapping him instead with a two-shot penalty.
That dropped him back to one-under-par, leaving him tied for 19th place, five shots behind the halfway leader, Australia's Jason Day, but still right in contention to win a fifth green jacket.
"I understand and accept the penalty and respect the committee's decision," Woods said in a statement before heading out to the practice range at Augusta National.
The decision not to disqualify Woods triggered an instant debate around the golfing world, with players and fans divided over whether he had got off lightly or should have withdrawn himself.
The players already on the course were seemingly oblivious to the simmering controversy as they tried to make up ground on what is traditionally known as moving day.
Conditions at Augusta National were ideal for low scoring on Saturday. The sun was shining brightly and there was barely any wind, allowing the backmarkers to attack the pins, which were in easier positions than the first two days.
The defending champion, American left-hander Bubba Watson, made six birdies in his round of 70, but handed back four shots with a pair of bogeys and a double to finish the day at two-over after scraping into the cut by a single stroke.
South Africa's Tim Clark, runner-up at the Masters in 2006, made a flying start to surge up the leaderboard, collecting five birdies in his first seven holes.
He joined a group of six other players, who were yet to tee off, at three-under.
Day, who tied for second on his Masters debut two years ago, was due to tee off at 14:45 local time (1845 GMT), leading by a shot from 1992 champion Fred Couples and Australia's Marc Leishman.
Argentina's Angel Cabrera was level with Americans Jim Furyk and Brandt Snedeker at four-under on a tightly congested leaderboard.