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.
"This is the first time … where I feel like that was a legit complete game."
The surging Terps earned a series sweep against the bottom-of-the-conference Golden Gophers.
The Golden Gophers walked four batters to send the Terps to their fifth straight win.