The 11th-ranked Ducks finished fourth in Friday's NCAA West Regional behind Stanford, Portland and UCLA, which also received an at-large bid on Saturday.
The men will be returning to the NCAA Championships after missing them in 2011.
Oregon was one of three Pac-12 teams that received an at-large bid. The Ducks were joined by the Bruins and Pac-12 champion Colorado. Stanford earned an automatic bid by winning the West Regional.
In addition to the Pac-12 teams, other schools earning at-large bids were Duke, Indiana, Michigan State, New Mexico, North Carolina, Princeton, Syracuse, Tulsa and Virginia Tech.
The Duck women earned an automatic bid to the NCAA Championships by winning the NCAA West Regional on Friday.