Danny Espinosa hit a three-run shot off Danys Baez with two outs in the ninth, one of the few bright spots for the Nationals. Stairs provided the other when he lined a single off Baez to become the 19th player with 100 pinch hits.
"A couple of good things happened at the end of the game," Nats manager Jim Riggleman said, hopeful the team could carry the momentum into Thursday night's game.
Vance Worley (2-0) threw six sharp innings and Raul Ibanez homered and had three hits for the NL East-leading Phillies, who have won 10 of 13.
Worley allowed one run and four hits, striking out a career-high seven batters in his fourth start in the majors. Worley is filling in for the injured Joe Blanton.
Marquis (3-1) gave up 10 hits and six earned runs in five-plus innings in his worst start of the season. His ERA rose from 2.62 to 3.66. Marquis was trying to go 4-0 for the first time.
"I was leaving balls up," Marquis said. "If I got it down, I got the contact I wanted."
Ibanez snapped an 0 for 35 slump with a pair of doubles on Tuesday, and is now 5 for 7 since the skid.
Ibanez gave Philadelphia a 1-0 lead when he connected on the first pitch from Marquis in the fifth. Ibanez hit a high drive deep into the seats in right-center.
The Phillies added two more runs in the inning on Shane Victorino's RBI single and Placido Polanco's sacrifice fly.
Adam LaRoche hit an RBI double to cut Washington's deficit to 3-1 in the sixth, but Philadelphia chased Marquis with four in the sixth.
Worley has allowed just one run and six hits in 12 innings in his two starts since coming up from Triple-A Lehigh Valley. He already has as many wins as Cliff Lee, one of Philadelphia's four aces.
On a chilly night at the ballpark, a crowd of 44,123 made it 152 straight sellouts in Philadelphia, including postseason play.
Riggleman was ejected in the fourth when he came out after LaRoche was upset with a called third strike. LaRoche dropped his bat at the plate and had a few words for umpire Alfonso Marquez, so Riggleman left the dugout and got the quick ejection.
"Adam doesn't say anything. He's quiet," Riggleman said. "So if he complained, I felt I had to."
NOTES: The Nationals said Michael Jacob Allen, the stepson of Davey Johnson and son of Susan Johnson, died Tuesday at 34 from infection and pneumonia in Orlando, Fla. Davey Johnson is the senior adviser to general manager Mike Rizzo. ... Nationals OF Jayson Werth went 1 for 4 against his former team. ... Nats LF Michael Morse was a late scratch because of right knee soreness. Laynce Nix took his place in the lineup. ... Marquis had thrown 15 scoreless innings before Ibanez homered. ... Espinosa leads all NL rookies with 18 RBIs.