Marcel White's layup with 1:09 to play put the Dolphins (3-9) ahead 66-65. After a miss by the Bulldogs (6-5), Omar El Manasterly made one of two free throws with 55 seconds left. Holder then came up with a steal and Andris Misters made one of two free throws with 10 seconds left.
Tyler Strange missed a 3-pointer at the buzzer and Gardner-Webb's three-game winning streak ended.
Misters added 14 points for Jacksonville with Kori Babineaux getting 13.
The Bulldogs shot 67 percent in the first half and led by as many as 14 before settling for a 43-32 advantage. In the second half, Jacksonville shot 57 percent to the Bulldogs' 35.3.