The Terps now control their own destiny for the top seed in the Big Ten tournament.
The Terps' Nick Dean, Jason Savacool and Ryan Ramsey have been dominant to start the season.
Cowles was the second and final Maryland player taken in the draft.
The Terps struggled to keep the 49ers silent, allowing runs in six straight innings.
Despite the senior day loss, the Terps are still in prime position to make the NCAA tournament.
The Terps walked off the Hoosiers in the first game, while Sean Burke took a no-hitter into the seventh inning of game two.
The Terps now sit tied for second place in the Big Ten.
Matt Orlando's double in the eleventh inning and six straight strikeouts from Ryan Ramsey set the Terps up for a monumental win.
The Terps picked up their 13th victory in their last 15 games.