The Wildcats will now move on to the 55th Annual NAIA Men's Soccer National Championship final site in Montgomery, Ala. They will compete at the Emory Folmer YMCA Soccer Complex from Dec. 2-7.
BU will next take on an Ashford team that also won in double overtime in the 105th minute to defeat Cardinal Stritch in its NAIA Opening Round home game on Saturday.
Baker outshot Midland, 24-14, with Ben Coyle taking a match high seven, but none bigger than his game-winner in the 106th minute.
The Warriors put the first goal on the board in the 10th minute, when Adam Wood scored his team high 23 goal of the season to put Midland up 1-0.
Then right before halftime, Chris Tuso sent a corner kick ball into the far side of the box and after each team knocked the ball back-and-forth, freshman Kyle Young slammed home the goal past keeper Lewis Wilcox.
Matt Bickley had five saves on the day and Wilcox had 10.