Virginia (56-11) will face defending national champion South Carolina in the Bracket 2 final. The Cavs would need to beat the Gamecocks on Friday and again Saturday to reach next week's best-of-three finals.
The loss ends an improbable postseason run for California (38-23), which started the year with its program scheduled to be dropped in 2012 for budgetary reasons. A $9 million fund-raising effort saved the program.
Kenny Swab singled and came around to score on a three-base error to start Virginia's big sixth inning.
Wilson (10-0) allowed five hits over his career-high 7 2/3 innings. Cal starter Dixon Anderson (4-4) took the loss.