He almost got what he wanted.
Laynce Nix added a pair of insurance runs with a single after Zimmerman's hit in the ninth.
The Nationals were working with a depleted bullpen after starter Tom Gorzelanny left Sunday's game after the third inning with an injured ankle.
"My mentality is always nine," Marquis said. "Obviously, with the bullpen having to eat up some innings yesterday, I obviously wanted to go as long as possible to freshen up their arms."
Roger Bernadina singled to start the inning before advancing to second on a sacrifice bunt by Danny Espinosa. Zimmerman's grounder rolled just out of reach of a diving Jeff Keppinger and into the outfield to allow Bernadina to score and chase Houston starter Jordan Lyles (0-5).
"I didn't hit it great, but I found a hole and it worked," Zimmerman said.
The Astros' rookie allowed five hits and four runs with six strikeouts in the longest outing of his career to remain winless in his ninth career start.
"I feel sorry for him losing that ballgame," Johnson said of Lyles. "He pitched a great ballgame. Pitched his heart out."
Lyles is staying positive while he waits for his first win.
"If I continue to have more outings like I did today, they will come often and a lot," he said of victories. "I have to continue to get better and keep making good pitches like I did tonight."
Morse homered in the fifth inning and Zimmerman's came in the seventh.
Marquis (8-4) yielded six hits and two runs with a season high-tying nine strikeouts to get his first win since June 10.
"I've been feeling pretty good all year," Marquis said. "I had a good sinker-slider combo tonight. I was able to get ahead early and get some quick outs."
Michael Bourn singled to start Houston's side of the eighth, but Marquis retired the next three Astros to end the inning and his night.
Closer Drew Storen allowed one hit in a scoreless ninth for his 25th save.
Lyles had retired seven straight before Zimmerman's homer that landed in the first row of the stands in right field with one out in the seventh inning and tied it 2-all. Morse followed with a single, but Lyles retired the next two Nationals to get out of the inning before pitching a perfect eighth.
"The kid was absolutely outstanding tonight," Houston manager Brad Mills said. "He really threw the ball downhill today. He threw everything for strikes."
"He pitched a great game and I thought he was in command all day long," Johnson said of Marquis. "I thought he made bad pitch to Lee with a guy in scoring position but other than that he was quite impressive."
Lyles didn't allow a hit until Morse's homer to left field on the first pitch of the fifth inning. He walked Bernadina to start the fourth inning, but faced the minimum through four thanks to a double play in that frame.
The first hit Marquis yielded was a single by Corporan with no outs in the third inning. He retired the next six Astros after that before the double by Michaels in the fifth inning.
Nationals infielder Jerry Hairston Jr., who had a broken bone in his right wrist, was activated from the disabled list on Monday, but did not play.
Buddy Lamothe, the Astros' 40th-round pick in this year's draft who is paralyzed from the waist down, was on the field with the team for batting practice before Monday's game. The Astros had their eye on the reliever from San Jacinto College before he was injured in a diving accident in May. Lamothe, who is recovering at a facility in Houston, hopes to play again one day. "Being out here just gives me a lot of hope to get back out here one day and pitch for the Astros," he said while on the field with his family and college coaches. "That'd be nice."... C Ivan Rodriguez (strained right oblique) is feeling better, but Nationals manager Johnson still isn't sure when he'll come off the disabled list. ... The Nationals hope that Gorzelanny will be able to make his next scheduled start after twisting his right ankle on Sunday in a home-plate collision. If he isn't, the Nationals could go with four pitchers in their rotation for a bit because of two upcoming off days. ... Houston OF Jason Bourgeois (right quadriceps strain) went 0 for 5 in a rehabilitation start at Double-A Corpus Christi on Sunday. He will join Triple-A Oklahoma City on Tuesday. ... Houston INF Matt Downs, who is on the paternity leave list, and his wife Leah welcomed their first child, a boy named Matthew Jr. on Monday.