It's also the Nationals' first series loss since these same two teams met in Washington from July 31-Aug. 2.
"We just ran into guys who threw the ball just as well as ours, and they got one or two big hits and we didn't," third baseman Ryan Zimmerman said after Saturday's loss. "People forget that that's a good team over there."
Gio Gonzalez stumbled in the first inning, yielding the Phillies a 2-0 lead early, but the Nationals' offense went quiet for the second straight night without cleanup hitter Michael Morse (right hand) and shortstop Ian Desmond (right hamstring).
Part of the credit is owed to two-time Cy Young Award winner Roy Halladay, who threw three innings of no-hit ball before Bryce Harper singled to right in the fourth.
"It's not a lull; just got a little beat up with Desi down and Morse down," manager Davey Johnson said. "I give credit to the opposition pitching. They pitch good here. It's not chopped liver over there. They're very talented."
Jimmy Rollins and Kevin Frandsen both reached to lead off the first and scored on Chase Utley and John Mayberry Jr. singles. Gonzalez settled down after that, and the Nats climbed back into it.
Roger Bernadina, Danny Espinosa and Kurt Suzuki recorded three straight one-out singles in the fifth. When Utley decided to go home with the play on a Gonzalez grounder to second with one out, it left the door open for Steve Lombardozzi to tie the game at 2 with a two-out single up the middle.
Espinosa singled to lead off the seventh but was stranded at third base, and Antonio Bastardo struck out the Nats' 2-3-4 hitters in the eighth. Philadelphia tacked on an insurance run in the eighth when Utley was hit by a pitch, stole two bases and scored on a sacrifice fly.
Halladay, 12-2 with a 2.55 ERA in his career against the Nats, scattered seven hits over as many innings, striking out six and walking one.
"Even in a season that hasn't really gone the way we want, it's important to go out and compete against those teams," Halladay said. "I don't think any of us are just going to roll over and give them games. We kind of want to make a little bit of a statement at the same time. We still want to play. We still want to compete. And we're not going to just give anything away."
And Gonzalez, who was bidding to become baseball's first 17-game winner, had a personal three-game winning streak snapped with the loss.
"They put it together," Gonzalez said of the Phillies. "Those guys can swing the bat, they know how to work the bat. The outcome was there. They were putting me out there, they were giving me a battle, and I was trying to battle back."
As for team streaks, the Nationals have lost more than three in a row just twice this season -- a five-game skid from April 26-May 1, and a four-game slide in June that included the Yankees sweep.
Sunday, against another Cy Young Award winner in Cliff Lee, they look to avoid that fate yet again.
"Luckily we haven't had a lot of them this year," first baseman Adam LaRoche said. "We've been really good at fighting back after we lose a couple, and haven't had that huge skid where everything falls apart. Again, I don't see it happening here."