Harper has been out since he slipped on a wet base and hyperextended his left knee on Aug. 12. The five-time All-Star has missed 42 games, and Washington hoped to get him back in the lineup on Monday to prep for the postseason. Instead he spent much of the day receiving treatment for flulike symptoms.
He could be back Tuesday night.
"Possibly. We just have to see how he feels," manager Dusty Baker said. "You hate to waste these days, but you also hate to push him out there when he's not ready. Hopefully, it's just an overnight thing."
Philadelphia would be an ideal place for Harper to return. In 38 games at Citizens Bank Park, Harper is batting .296 with 12 homers.
Harper was in the clubhouse after the game but did not speak to reporters.
Odubel Herrera homered for the Phillies, who have been playing better of late but entered one game ahead of the Giants for the worst record in baseball.
"The bats have been silent for a few days," manager Pete Mackanin said. "We just couldn't get anything going."
Cole (3-5) struck out five and walked two while giving up six hits.
"He stayed out of the middle of the plate," Baker said.
Sean Doolittle pitched a perfect ninth for his 21st save in 21 chances with the Nationals since being acquired from Oakland on July 16.
Aaron Nola (12-11) allowed Taylor's two-run drive in the second but otherwise pitched well for Philadelphia. He struck out nine, walked two and allowed five hits in six innings.
"He pitched extremely well," Mackanin said. "When he pitches, we all expect to win."
Taylor's 17th homer this season, a 398-foot blast to left-center, gave the Nationals a 2-0 lead. The center fielder, pushed into a starting role when Adam Eaton tore his ACL in April, will be expected to continue producing in the playoffs.
"We need that," Baker said.
Cole kept the Phillies off the board until Herrera snapped an 0-for-17 skid with a solo shot, his 14th, on a 1-2 pitch with two outs in the fourth.
Werth's eighth-inning groundout plated Zimmerman to put Washington on top 3-1.
The Nationals struck out 13 times.
Doolittle has pitched to a 0.86 ERA with the Nationals while holding opponents to a .155 average.
PHILLY SLUMPING I
The Phillies have lost 23 of their last 30 to Washington.
PHILLY SLUMPING II
Rookie Philadelphia slugger Rhys Hoskins went 0 for 4 and has one hit in his past 15 at-bats.
Nationals: LHP Gio Gonzalez (15-7, 2.68) looks to extend his success in Philadelphia, where he is 6-3 with a 2.44 ERA in 12 starts. Gonzalez, a former Phillies farmhand, has never allowed more than three earned runs at Citizens Bank Park.
Phillies: RHP Jake Thompson (2-2, 4.14) is 1-0 with a 0.87 ERA in his last two outings.
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