Wesley Person scored 28 points, including six 3-pointers, and Jordon Varnado added 16 points for Troy (5-5), which controlled the boards 42-35 to snap a two-game skid. Walton's rebounds fell just one shy of Troy's single-game Division I record.
The Trojans took a 46-28 advantage into the break but had to hold off a second half rally to clinch the win.
Paine, a Division II program, chipped away at the gap throughout the second half, tying at 71 on a 3-point play from Christian Nobles with 3:56 to play. Troy edged back into the lead with Person's layup, which sparked a 6-0 spurt and the Trojans hung on.
Denzel Dillingham's 19 points led three Paine players in double figures.