The win is the Flyers' second over a ranked opponent this year after dropping then-No. 25 DePaul 92-80 on Nov. 10.
Dayton is 4-0 for the first time since 1992-93.
The Flyers led by as many as eight in the first half and went into halftime up 33-30. The Commodores' Tiffany Clarke hit consecutive buckets to open the second half, vaulting Vanderbilt (3-1) ahead.
The advantage lasted about five minutes until a Hoover jumper sparked an 11-0 Dayton run that put the Flyers up 48-43. Vanderbilt forced a tie at 52-all with 8:17 left, but Hoover hit two free throws shortly thereafter and the Commodores never regained the lead.
Clarke scored a game-high 23 points for Vanderbilt.