Niese (5-6) was on the disabled list for nearly two months with a partially torn rotator cuff before coming back on Sunday at Arizona. The left-hander won consecutive starts for the first time this season.
He allowed six hits, walked one and hit one batter Friday. Niese and three relievers combined to strike out 13, running New York's two-game total to 28.
The Mets acquired d'Arnaud in an offseason trade that sent NL Cy Young Award winner R.A. Dickey to Toronto. He broke his foot early in the season while playing for Triple-A Las Vegas.
"We're all excited to see Travis," New York manager Terry Collins said. "Like a lot of these guys, there is a huge buildup taking place. Some of the reports are pretty impressive."
Said Niese, who pitched to d'Arnaud in a rehab start: "It was good. He received the ball well. I liked the way he hit better."
Byrd and Davis connected on consecutive pitches from Ian Kennedy in the third inning. Murphy hit a two-run shot an inning later to give the Mets a 5-1 lead.
Davis, who has had a second-half resurgence, hit just his second homer since he was recalled from the minors on July 5.
"I finally caught up to one and drove it out of the yard," he said. "To be honest, it felt good. I have been getting jammed with fastballs in lately, and I finally got to one."
Byrd has driven in six runs in his past three games after going without an RBI for the previous 13. Before he homered, Murphy had just one extra-base hit in his past 20 games.
Davis has four homers off Kennedy (4-9) in only nine at-bats.
"I wasn't as sharp as I wanted to be command-wise all night, which explains why there were so many home runs," Kennedy said.
Kennedy, acquired in a trade from Arizona on July 31, allowed five runs on seven hits over 4 2/3 innings in his third start for San Diego. The righty, who has allowed 22 home runs, struck out seven and walked four.
New York's Anthony Recker, starting in place of catcher John Buck, who went on the paternity list, had a career-best three hits and also reached on a walk.
San Diego has dropped eight of 10 and fell into last place in the NL West with the Giants' win over Miami.
Byrd led off the third inning with his 19th home run, and, on the next pitch, Davis hit homer No. 7. It was only the second time this season that New York has hit consecutive home runs.
Will Venable ran his career-high hitting streak to 13 games with a solo homer in the third. Venable's 16th home run extended his career high.
Yonder Alonso added an RBI single in the eighth and Jedd Gyorko had three hits for San Diego, including a double. Gyorko has nine hits in his past six games, six for extra bases.
Kennedy lost for the first time (4-1) against the Mets in six career starts. ... Padres LF Carlos Quentin is expected to miss another seven to 10 days with a strained right knee. Quentin received a second opinion from the Kerlan-Jobe Orthopaedic Clinic in Los Angeles on Thursday, and San Diego manager Bud Black said the result was "the same findings that our team doctors had." ... Slumping New York rookie CF Juan Lagares was held out of the starting lineup. Lagares is hitting .210 (13-for-62) in August and is hitless in his past 13 at-bats with five strikeouts. ... The teams continue their four-game series Saturday night with Mets RHP Jenrry Mejia (1-2, 2.22 ERA) set to face Padres RHP Edinson Volquez (8-10, 5.80).