Anthony Rendon, who is one of the top candidates to be the No. 1 overall pick in next month's Major League Baseball draft, led off the 10th inning with a double to left field that short-hopped the wall. Michael Ratterree was then intentionally walked, setting up Manuel's game-winning single that scored Rendon.
Rice won its fourth tournament title in six seasons. The Owls have a 41-19 record.
Houston starter Jared Ray, who had thrown only 16.2 innings all season, went eight innings against Rice, giving up three runs. Rice's Tyler Duffey threw 4.2 innings of scoreless relief, striking out seven.
Rice has won 15 straight games against Houston. The Cougars finish their season with a 27-32 record.