Manager Dusty Baker said Harper would undergo an MRI on Sunday and that the Nationals would know more about the extent of his injury then.
"He was in obvious pain, and he was praying, and I was praying too," Baker said.
While running out a ground ball to the right side of the infield in the first inning of a 3-1 win over the San Francisco Giants on Saturday, Harper avoided contact with first baseman Ryder Jones, then his left foot slipped on the base. His leg buckled, he went airborne, and he fell to the ground as his helmet went flying.
"I'm asking for prayers that it's not serious," Baker said.
Harper was seen with the knee wrapped in the clubhouse after the game, and he walked with a limp as he left the stadium, according to MLB.com.
He clutched at his left knee after going down and was attended to by trainers. The star outfielder put no weight on his left leg as he was helped off the field by hitting coach Rick Schu and head athletic trainer Paul Lessard.
The game began just after 10 p.m., following a three-hour rain delay. It was raining steadily when Harper's injury happened.
Major League Baseball was in control of weather decisions, because it was the Giants' final trip to Washington this season. The series opener Friday was postponed after a lengthy rain delay to be part of a day-night doubleheader Sunday, which added to the league's incentive to get Saturday's game in.
Saturday's tilt was unlikely to have an impact on the playoff race, as the Nationals lead the NL East by 14.5 games and the Giants are out of contention. At most, the game could have an effect on home-field advantage in October.
Even though first baseman Ryan Zimmerman is having an All-Star season, Washington's title hopes hinge largely on Harper's health. The 2015 MVP is having another spectacular season, hitting .326 with 29 home runs and 87 RBIs this season.
Harper didn't last long in his 106th game of 2017 and was replaced by Andrew Stevenson, who took over in center field, with Brian Goodwin moving to right. Despite many fans waiting out the delay, the stadium went eerily silent in the minutes after Harper's injury.
Because of a bevy of injuries, the Nationals have used 12 outfielders this season. They have been without Adam Eaton since late April because of a torn ACL in his left knee that ended his season, Jayson Werth since early June because of a bruised left foot and Michael Taylor since July due to a right oblique strain.
"There aren't many organizations that have 12 outfielders that they can really rely on and count on," Baker said Friday. "Boy, that is a lot, especially when you only play three at a time. I'm just glad we have them."
The Nationals are running away with the division, despite those injuries -- and more to starters Stephen Strasburg and Joe Ross, relievers Shawn Kelley and Koda Glover and shortstop Trea Turner. But a long-term injury to Harper would be far more trouble to Washington's postseason hopes.
Harper is under contract through next season and can be a free agent in the winter of 2018.
Information from The Associated Press was used in this report.