Seawolves had come so close to their first trip to the tournament, fighting back after digging a four-goal hole in the first half to tie the score with 4:59 left, but it was Albany that took a 9-7 victory at Boston University's Nickerson Field for its second consecutive conference title.
"It's awesome to get here, but our goal was to win and to get into the NCAAs, and we didn't reach our goal," said America East Player of the Year Claire Petersen, who tied it at 7 and erased what had been a 5-1 deficit.
But Albany's Maureen Keggins scored with 3:52 to play and Amanda Pollock clinched it with 11 seconds remaining.
"It's disappointing, I'm not going to lie," said Stony Brook coach Joe Spallina, whose team won 10 more games than the previous year, the nation's best turnaround. "We set a goal at the beginning of the season to get to NCAAs and we didn't do enough to get that done."
Petersen and Demmianne Cook each had two goals and an assist for Stony Brook (14-5). Mel Rorie had three goals and Jess Antelmi two for Albany (12-5).
Petersen finished with 42 goals and 59 assists for 101 points, becoming the first Stony Brook women's lacrosse player to accomplish the feat. Cook had a school-record 68 goals, which currently leads the nation.
After Cook scored to make it 1-1, Albany scored four consecutive goals, with Rorie making it 5-1 with 11 seconds left in the first half. Petersen scored with two seconds remaining to bring the Seawolves within three.
"I felt like they were in a trance early on," Spallina said. "But we're fighters. We have good kids who aren't just going to lay down and play dead."
SBU trailed 7-4 with less than 13 minutes left, but Michelle Rubino and Emily Mercier scored before Petersen tied it.