Chen, a junior from Bradenton, Fla., finished at six-under 274 to follow USC sophomore Annie Park as the individual champion.
Chen is the fifth USC player to win the title, joining Park, Dewi Claire Schreefel, who won in 2006, Mikaela Parmlid (2003) and Jennifer Rosales (1998). USC is tied with Arizona State for most women's golf champions.
USC finished two shots behind team champion Duke, which posted a four-day score of 10-over 1,130. UCLA was third at 1,145.
The Trojans began the final round six shots behind Duke.