Stony Brook led by more than 10 points at halftime, but Towson rallied back to hold the Seawolves scoreless in the second half and took home a 35-21 win on Saturday at LaValle Stadium.
It was the first home conference matchup for Stony Brook (1-3) in the Colonial Athletic Association.
Following a performance against Villanova last week that saw Stony Brook total a season-low of 87 yards rushing in a 35-6 loss, the Seawolves rushed 43 times for 142 yards against Towson. The Seawolves are without key players Marcus Coker, who will miss the season with an abdominal injury, and Reuben Johnson, who suffered a season-ending knee injury.
Stony Brook was led by junior running backs James Kenner, who totaled 87 yards, and Jameel Poteat, who finished with 72. Quarterback Lyle Negron finished 12 of 16 for 118 yards.
"I thought our preparation was great this week," head coach Chuck Priore said in a statement. "It was a hard-fought game and we probably had too many miscues."
Villanova entered the game ranked the No. 2 team in the FCS, while Stony Brook entered the game at No. 23.
"Since they're the second or third-best team in the country, I don't think we're that far off," Priore said. "I thought we set the tone early with our running game. This definitely is one of those games where it looks a lot different than the score indicates."