Murphy, who homered earlier, drove in the decisive run with a 10th-inning double as the Nationals defeated Atlanta 4-3 Monday in the 20th and final home opener for the Braves at Turner Field.
"It was like the game telling me, 'Welcome back,'" said Baker, who was let go by the Cincinnati Reds after the 2013 season. "There were a lot of highs and lows in that game."
The Nationals tied it in the ninth inning to spoil things for the crowd of 48,282, then won thanks to an unearned run after second baseman Gordon Beckham threw away a grounder by Ryan Zimmerman with one out.
Murphy went the opposite way against lefty reliever Eric O'Flaherty (0-1) for a quick payoff on the three-year, $37.5 million contract he signed as a free agent after hitting seven homers in the postseason for the New York Mets last year.
The Nationals' biggest move, though, may have been hiring Baker after the team underachieved under manager Matt Williams despite a loaded roster.
"I was flattered that they gave me the ball for my first victory in a Nationals uniform," said Baker, who took teams to the playoffs as manager of the San Francisco Giants, the Chicago Cubs and Cincinnati. "It can go to the house with all the other (balls). I don't think I've lost the first game with a team."
It was almost the Braves, though, who started the season with a victory.
Atlanta closer Jason Grilli, who sustained a ruptured Achilles tendon last July, nearly got a save in his return despite the Nationals loading the bases with no outs in the ninth inning on a walk, a single and a perfect bunt.
"It was a tough play at the plate there, you know?" Braves manager Fredi Gonzalez said. "That's why you send those runners. First of all, you've got to get a good throw and you've got to make a great tag and it's tough. It's not as easy as you think."
Baker said, "Inciarte made a heck of a throw, and Jayson made a heck of a slide. They got there at the same time, and A.J. never really had the ball."
The Braves had gone ahead in the eighth inning as Adonis Garcia drew a four-pitch walk from Shawn Kelley with the bases loaded. It came after Washington reliever Felipe Rivero gave up a walk and a single and hit a batter.
Until the bullpens took over, all the scoring came on solo homers, as both Max Scherzer for the Nationals and Julio Teheran for the Braves were stingy with baserunners.
Reigning National League MVP Bryce Harper and Murphy went deep for the Nationals, while Freddie Freeman and Garcia connected for the Braves.
Harper's first-inning homer, which was lofted to right field on a 2-2 slider, was his fifth on Opening Day in four seasons and his 14th against the Braves. He hit .369 with six homers and 16 RBIs against Atlanta last season.
The first two hits off Scherzer were homers. Freeman went deep to center field in the first inning on a 2-2 fastball, and Garcia's homer to left field in the fourth came on a hanging 0-2 slider.
"I made a mistake to Garcia, but overall I thought I did some good things," Scherzer said. "It was the first time I've faced Freeman, and we're going to have some battles."
Scherzer, who finished last season with his second no-hitter of the year, gave up three hits and two runs in seven innings. He struck out seven and walked two, throwing 104 pitches.
Teheran threw 102 pitches in his six-inning outing, giving up five hits and two runs, walking three, throwing a wild pitch and striking out four. Murphy's homer to center field came on a 2-0 fastball.
"He had a great outing, he really did," Gonzalez said of Teheran matching Scherzer.
Blake Treinen (1-0) threw a hitless bottom of the ninth to earn the win, then closer Jonathan Papelbon pitched a perfect 10th inning to record the save and get Washington's season off to a good start.
The Braves will move into a new suburban ballpark in Cobb County next season. This wasn't the way they wanted their final season at Turner Field to start.
NOTES: Nationals CF Ben Revere left the game after aggravating his ribcage on a fourth-inning swing. "We took him out as a precaution," said manager Dusty Baker, who called Revere day-to-day. ... The series concludes Wednesday night after a day off Tuesday, with RHP Steven Strasburg starting for the Nationals against RHP Bud Norris, making his Braves debut. ... RHP Julio Teheran, who started his third consecutive opener for the Braves, will pitch twice in the first four games because of two off days. ... LHP Gio Gonzalez is slotted fifth in the Nationals' opening rotation and won't start until next Monday against the Braves at Washington in the opener of a four-game series. ... The Nationals were 4-5 against the Braves in Atlanta last season but 10-0 at home. ... It was just the third time in the past 11 years that the Braves opened at home. ... The Nationals (19-4-4) had the best spring training record, while the Braves (6-16-6) had the worst.