Del Conte said the Owls will begin a nationwide search for a replacement.
Wilson was 219-246 in 16 seasons. He won more games and coached more games than any other Rice coach. His 16 years at the helm also set a school record.
He led the team to three NIT appearances. He won a career-high 22 games in 2004, and his 1998-99 team won 18 games after winning just six the year before.
The Owls finished the season with a 59-50 loss to Southern Miss in the first round of the Conference USA tournament Wednesday night.
Wilson, a former player for the Owls, spent a year as an assistant in Stanford in 1992 before becoming Rice's 22nd head coach.
Last year, Wilson coached Conference USA Player of the Year Morris Almond, the nation's third-leading scorer and first-round NBA draft pick of the Utah Jazz.