The Blue Devils (2-1) made 3 of 6 field-goal attempts in the extra session after struggling to find the range during regulation.
Fredonia State won the tip to start overtime and promptly scored the first five points. Chris Donahue made a three-point basket and Tim Anderson had a steal and a layup to give the Blue Devils the lead for keeps.
Taha Alassari made two free throws to tie the game with 12.6 seconds left in the second half.
D'Youville was unable to get off a shot in their final possession. A desperation shot at the buzzer by the Blue Devils missed the mark.
Anderson finished with 19 points and six assists, Alassari had 15 points and a team-high nine rebounds, and Donahue added 11 points.
Alassari also was credited with three steals, and Kyle Gordon grabbed eight rebounds.
The Blue Devils are back in action Nov. 29 at Buffalo State.