The Nationals announced the injury as a strained left hamstring and said Hernandez will be re-evaluated Thursday.
Hernandez had been enjoying an impressive spring, hitting .308 and all but guaranteeing himself the starting second baseman's job come Opening Day.
If he is forced to miss any considerable time, Washington likely would turn to veterans Ronnie Belliard and Willie Harris to fill in at second base. The injury also could open the door for another middle infielder to make the Opening Day roster. Alberto Gonzalez, Alex Cintron and Jose Castillo have all been in camp trying to win a spot.
Nationals 6, Braves 3
Needing an impressive start to help keep his slim hopes of making the Opening Day rotation alive, Collin Balester delivered.
Balester allowed two runs and four hits over five efficient innings, throwing only 55 pitches in the process. The right-hander retired the first eight batters he faced before faltering slightly the second time around the order (Chipper Jones clubbed a two-run homer in the fourth).
Balester threw first-pitch strikes to 12 of the 19 men he faced.
"This game is simple if you just throw strikes," he said.
Despite his best efforts, Balester may have run out of time to crack the Opening Day rotation. Rookies Jordan Zimmermann and Shairon Martis each have dazzled this spring, while Balester entered Wednesday night's start with a 7.80 ERA.