The two-time defending NL champions are off to a 6-1 start, their best since opening the 1993 pennant-winning season 7-1.
But now they might be without Rollins. The three-time All-Star shortstop and 2007 NL MVP strained his right calf while running in the outfield during pregame warmups. He already had been introduced in the starting lineup.
"I think a calf takes a while to heal," manager Charlie Manuel said. "He seemed in pretty good spirits."
All-Star right fielder Jayson Werth also left in the sixth because of soreness in his left hip.
"I'll be fine, more precautionary than anything," Werth said.
Cole Hamels (2-0) earned the win despite another so-so effort. He allowed four runs and six hits in 5 2/3 innings. The lanky left-hander is trying to bounce back following an inconsistent year after a dominant postseason in 2008.
"Unfortunately I wasn't able to go as deep as I'd like," Hamels said.
Despite losing Rollins, their leadoff hitter and catalyst, the Phillies continued their torrid hitting. They're averaging 7.1 runs and 11 hits per game.
The Phillies celebrated the franchise's seventh pennant during a pregame ceremony, then earned their first victory in a home opener since 2005.
Led by the Phanatic, their furry green mascot, players entered the field from Ashburn Alley behind the stands in left-center field. They walked through the crowd and onto a red carpet that stretched from the warning track to the infield.
Manuel raised the 2009 NL championship flag on the concourse behind the brick batter's eye. Players were introduced to rousing ovations and the U.S. Navy parachute team delivered the first balls.
"We had them on the ropes, but when you have a chance to put a team away and don't do it, it's tough," Nationals first baseman Adam Dunn said.
Marquis (0-2) allowed seven runs -- six earned -- and six hits in 4 1/3 innings. The right-hander, who signed a $15 million, two-year contract with Washington as a free agent, was an All-Star with Colorado last season.
The Phillies came back from a 4-0 deficit, scoring twice in the fourth and chasing Marquis during a five-run fifth. Carlos Ruiz started the fifth with a single. Hamels tried to sacrifice and reached safely when catcher Ivan Rodriguez's throw to second bounced into center field for an error.
Juan Castro, filling in for Rollins, hit an RBI double to deep left-center. Polanco followed with a two-run single to right-center to put the Phillies ahead 5-4, and Utley added a two-run shot off the foul pole in right.
"I thought we had some pretty good at-bats," Utley said.
Willingham homered leading off the second, and Washington added three runs with two outs in the fourth.
Hamels nearly escaped trouble after giving up a single to Cristian Guzman and nicking Dunn's jersey with a pitch. He struck out Willingham on a 3-2 pitch, painting the outside corner with a 92 mph fastball. He blew a fastball past Ian Desmond for the second out, but Rodriguez followed with an RBI single to make it 2-0.
After Adam Kennedy walked to load the bases, Marquis lined a two-run double out of the reach of leaping third baseman Polanco.
The Phillies answered with two in the bottom half. Polanco hit a one-out single, Utley walked and Ryan Howard hit an RBI single.
Nationals manager Jim Riggleman went out to talk to Marquis and was ejected by plate umpire Paul Schrieber, who went to the mound to speed up the conversation. Werth drove in a run with a grounder to third to cut it to 4-2.
Hamels helped the Phillies win their second World Series title in '08, earning MVP honors in the NLCS and World Series. But he struggled to match that success last year, going 10-11 in the regular season and 1-2 in the postseason.
The Phillies had their 43rd consecutive sellout in the regular season. ... Phillies first base coach Davey Lopes rejoined the team following the death of his brother earlier this month.