The incident took place near the 17th tee shortly before second-round play was stopped due to stormy weather.
The trees crashed to the ground near spectators, but organizers said that there had been no injuries.
"Augusta National Golf Club can confirm that no injuries were reported from three trees that were blown over to the left of the No. 17 tee due to wind," the club said in a statement.
"The safety and well-being of everyone attending the Masters Tournament will always be the top priority of the club. We will continue to closely monitor weather today and through the tournament."
Shortly after the trees fell, organizers announced that play was halted and spectators were evacuated from the Augusta National course, which was being hit with gusting winds.
An announcement said thunderstorms were approaching the area with heavy winds and lightning.
Towering pine trees are a trademark feature of the famed, 7,545-yard course, the world's only layout to host a men's major golf tournament every year.
There were 39 players who were unable to complete their second rounds put will attempt to do so when play is scheduled to resume at 8am Saturday.
Severe storms are in Saturday's forecast as well, but officials hope to be able to make the cut to the low 50 and level for the final two rounds.
After a 21-minute stoppage Friday brought a return to competition, play was suspended for a final time at 4.22pm after trees fell near the 17th hole.
Tournament officials said no one was injured.
Spectators were evacuated and players removed from the course.
American Brooks Koepka had the early clubhouse lead, three strokes ahead of Spain's third-ranked Jon Rahm, who still had the back nine to finish, and four strokes ahead of US Amateur champion Sam Bennett.
Four-time major winner Rory McIlroy fired a 77 and was all-but assured of missing the cut while Tiger Woods was on the cutline at 2-over with seven holes remaining.
