Twenty-six players started their rounds in the curtain-raiser event for the year's first major which begins on Thursday.
"The safety of everyone on our grounds was the determining factor in the decision to close the course and cancel the Par 3 contest," Augusta National Chairman Billy Payne said in a statement.
"We share in the disappointment of our patrons, but the safety of everyone on our grounds is always our primary concern."
Former Masters champion Mike Weir of Canada fired a hole in one and moved joint top of the leaderboard on three under par after seven holes before organisers brought the players off the course.
Monday's practice session was also called off and more heavy rain is forecast overnight.
(Reporting by Ed Osmond; Editing by Frank Pingue)
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