Stony Brook's fifth-inning rally came up short as they lost the second game, 6-5, to third-seeded Albany.
Freshman Allison Cukrov, who set a Stony Brook record with 13 shutouts this season, allowed six runs in two-plus innings, before being relieved by Christine Lucido, who allowed three hits in four innings.
Katie Wambold's RBI single capped a four-run third inning that gave the Great Danes a 6-2 lead.
Shayla Giosa's two-run homer in the fifth inning pulled Stony Brook within a run, but Albany (36-13) held on, eliminating the Seawolves.
Lauren Maloney went 3-for-3 with an RBI and Bernadette Tenuto was 2-for-3 with a run and an RBI for Stony Brook (36-17-1), which tied the program's single-season record for wins.
Top-seeded Boston University had beaten them, 7-3, in the earlier game.
Whitney Tuthill scattered 10 hits in a complete game to lead the Terriers (39-14).
Jayme Mask scored three runs and Emily Roesch had two RBIs.
Tenuto was 2-for-4 with two RBIs for Stony Brook.
Cukrov allowed seven runs in 62/3 innings in the loss.
Stony Brook's Maloney and Tenuto were named to the all-tournament team.