James Sylvester hit a 3-pointer with 2:11 left in overtime to put Coppin State up 93-90, but the Eagles did not score again.
Watson sank two free throws with 43 seconds left to pull the Dons within one, 93-92, but missed a layup with 12 seconds left. Derksen came down with the rebound and his putback gave San Francisco the lead. Derksen stole the ball from Joshua Treadway with a second left to seal the win.
Sylvester hit two free throws with 4 seconds left in regulation to force overtime.
Watson finished with 31 points and Derksen 23 to lead San Francisco (6-4).
Terry Harris Jr. scored 27 points to lead Coppin State (2-9).