The Cavs slumped badly in the second half of the season and finished 1-5-2 in the eighth spot in the nine-team conference -- its worst finish ever.
To make matters worse, star Yannick Reyering was lost for the season with a knee injury in the final game of the ACC regular season.
Virginia beat last-place N.C. State, 4-1, in a play-in on Tuesday but was missing three key players -- Neil Barlow, Matt Mitchell and Reyering -- for the BC game.
Jamie Melas scored the game-winning goal in the 64th minute for top-seeded Boston College.
"I am proud of the way we fought and how hard we played," Virginia coach George Gelnovatch said. "We were without Matt Mitchell, Yannick Reyering and Neil Barlow and had played 90 minutes the day before, so I think that took its toll on us. Now we are looking forward to the NCAA Tournament."
At 11-7-2 overall and 9-1-0 in non-conference play, the Cavaliers should get an at-large bid to the NCAA Tournament.