Headley, the iron man of the injury-plagued Padres, started 42 of the first 43 games prior to his much-needed day off.
Manager Bud Black and Headley agreed that it would be best for Headley to take a short rest in order to avoid a bigger problem down the road.
"He's great about letting the player tell him how you feel," Headley said. "I didn't anticipate it being a big deal. It was a good day to get off of it".
Black can be forgiven if he jumps at the slightest hint of a player injury.
The Padres have 13 players on the disabled list, with five out for at least 60 days, including pitcher Cory Luebke, who underwent Tommy John surgery on Wednesday. San Diego has used an NL-high 39 different players this season.
So Black and Headley decided to proceed with extra caution.
"I came in early [Wednesday] and got treatment," Headley said. "It's fine. I would say I'm as 100 percent as you are during the season."
Headley, who leads the team with five homers and 20 RBIs, kept his activity to a minimum on Tuesday and said his back felt much better.