When asked about the incident by reporters after the game, Williams attributed Harper's "inability to run 90 feet" as the reason for the benching.
"We made an agreement," Williams said. "He and I made an agreement. This team made an agreement that when we play the game, that we hustle at all times, that we play the game with intensity and the willingness to win."
Harper, who finished the game 0-for-3, has missed time recently with a quad injury, though he told the Washington Post the injury felt "fine" Saturday. He told reporters after the game that he respected Williams' decision, calling it "part of the game."
Nationals general manager Mike Rizzo told the Washington Post after the game that he backed Williams' decision. "I unequivocally support the manager's decision 100 percent," he said.
Harper is expected to be back in the lineup Sunday.
Information from The Associated Press was used in this report.