The All-Star took an awkward tumble while throwing home, held his left leg while down on the ground and then gingerly walked off the field.
"I've had problems with my left knee before -- I've had surgery on it," Harper said after the game. "So you know, it was definitely really scary."
Nationals manager Matt Williams said the strain was mild and that Harper would be re-evaluated Friday. He gave no estimate on how long Harper might be out or whether he would need to go on the disabled list, although Harper indicated he might be day-to-day.
"Be smart about it, of course," Harper said. "I want to be in there, but if I don't feel right tomorrow, then maybe taking that day off might help me a little bit."
The mishap occurred on wet turf in the sixth inning after an earlier rain delay at Nationals Park.
"That wet surface played a big part in that, and it's a bummer it happened," Harper said.
Said Williams: "Conditions are conditions."
Harper suffered the strain as he fielded a single by Asdrubal Cabrera and tried to throw home. As he planted his right foot, it slipped and his left leg buckled. The throw went wild.
The slugger stayed down on the grass for a few minutes. He eventually rose to his feet and walked off under his own power, escorted by members of the Nationals' training staff.
Entering Thursday, he was batting .344 with 22 home runs and 53 RBIs. He went 1-for-3 with an RBI against the Rays before exiting.
A two-time All-Star at 22, he has dealt with several lower-body injuries throughout his career and had surgery his left knee after the 2013 season for a bursa sac.
Harper also missed roughly a third of last season with a thumb ligament injury.
A prolonged absence would add to the injury difficulties for the Nationals.
Doug Fister (2-3) came back from a month out with forearm tightness Thursday but allowed five runs in 5 1/3 innings. Starter Stephen Strasburg (neck tightness) could return to the team after his next bullpen session.
"It's time to step up. Everybody," Williams said. "We look forward to doing that tomorrow."
Information from The Associated Press was used in this report.