Zimmerman, who missed 53 games with plantar fasciitis in his right foot this season, showed obvious discomfort while running down the line.
"Same foot, same sort of thing,'' Zimmerman said after the Nationals' 7-1 loss.
He is scheduled for an MRI on Monday to determine the severity of the injury.
Zimmerman, 34, is batting .246 with three home runs and 15 RBIs in 33 games.
The Associated Press contributed to this report.