In a statement, the school did not say if he resigned or was fired.
"Coach Westphal is among the most outstanding people I've known or had the pleasure to work with," said athletic director John Watson. "We extend him our best wishes for the future."
The Waves, a member of the West Coast Conference which also includes 5th-ranked Gonzaga, had a dismal overall record of 7-20 this season. They went 3-11 in league play and lost, 85-72, in the first round of the WCC Tournament on March 3.
Westphal played 12 NBA seasons with Boston, Phoenix, New York and Seattle and was a five-time All-Star. He took over at Pepperdine in April 2001 after NBA coaching stints with Phoenix and Seattle. He also was a coach at the college level at George Mason.