The win, number 63 on the season, guaranteed the Phillies' season would not end with triple-digits in the loss column.
"When I said that 98, 99 or 100 losses didn't matter, I lied. I admit it," Phillies manager Pete Mackanin said.
Thompson limited the damage from the Nationals' offense even with Harper inserted back into the lineup for his first game since Aug. 12. Harper went 0-for-2 with a walk before he was replaced by Victor Robles in right field in the bottom of the fifth inning.