Scott Podsednik started the game off with a walk before Ryan Theriot reached on an error by Marquis, who had a tough time fielding a bunt.
With Andre Ethier at the plate, Theriot stole second, and Podsednik scored on a throwing error by catcher Wil Nieves. After Ethier walked, James Loney singled to left, scoring Theriot.
Marquis said he was not thinking that he would have a repeat performance like he did against Milwaukee, but realized he needed to improve on the mound.
"I put myself in trouble with the walks," Marquis said. "There was one play where I didn't pick up the ball. There was an out I gave away there. I have to make sure it doesn't happen again."
Marquis was able to get two outs before Jamey Carroll singled to center field to drive in Ethier and Ronnie Belliard. Marquis threw 32 pitches -- 18 for strikes -- in the first inning.
Marquis acknowledged that he was a little nervous, but, as his custom, he didn't give an excuse for his ineffectiveness.
"It was nothing out of the ordinary," Marquis said. "I'm excited to be back. I wish it would have turned out a little bit better today. I'll work my butt off to do little better and I'll have better results next time."
After the first inning, Marquis allowed one run in three-plus innings. He said he was able have more success with his breaking pitches.
"I was locating my offspeed pitches a little bit better, keeping it in the bottom half of the strike zone -- throw more quality strikes," Marquis said.
The Nationals made it a game in the second inning, when Michael Morse and Justin Maxwell hit back-to-back home runs against left-hander Ted Lilly.
"I felt a little flat," Lilly said. "I thought my ball was a little flat, so I had to work to try to get back on top of it and get a little plane to it. ... The fastball that I threw to Mike Morse was decent, and he pulled his hands inside and kept that ball fair. A lot of times guys hit that ball, maybe square it up and hit it well, but hit it foul. And he was able to keep his hands inside there. The other pitch was a slider."
Manager Jim Riggleman thought the Nationals had a chance to make a comeback after they made it a two-run game.
"At that point, Jason was putting up some zeros," Riggleman said. "It just got away from us in the end. Lilly got better as he went along. He found his curveball, it looked like. It was like that with Craig Stammen a couple of times. He didn't have his curveball until the third or fourth inning. It appeared Lilly really locked in on that and stifled us a little bit with some great breaking pitches. Early on, we had our chances. It was a great day to get the ball in the air, because it was flying."
Los Angeles added to its lead in the fourth inning off Marquis. With one out, Carroll scored on a double by A.J. Ellis.
Marquis lasted four-plus innings and allowed five runs, but only two were earned because of the errors by Nieves and himself.
The Nationals scored one more run off Lilly, a sacrifice fly by Alberto Gonzalez, before Los Angeles made it a three-run game off Miguel Batista, who allowed an RBI single to Jay Gibbons.
The Dodgers added to the lead in the bottom of the eighth inning, when Washington reliever Drew Storen allowed a two-run single to Reed Johnson.
With the loss, the Nationals head back to Washington with a 49-63 record. They finish the road trip with a 3-4 record.
"It's tough. We battled, but the record doesn't show it," shortstop Ian Desmond said. "We played some good games against Arizona. We played a [good game in Los Angeles]. Today, we kind of gave it away."