Kendrick singled twice and scored on Martinez's drive in the fifth inning off Mike Pelfrey (5-9). Martinez, a Rule 5 pick from Washington, added a sacrifice fly in the seventh for a career-high four RBIs.
Ryan Howard hit a run-scoring single in the first and Philadelphia took two of three from the NL East rival Mets for the fourth time this season. Jimmy Rollins had a two-run single in a three-run eighth aided by Jason Bay's error in left field and reliever Pedro Beato's three walks.
Those eighth-inning runs provided a needed cushion when the Mets took advantage of four walks and a hit batter to score three in the bottom half - Kendrick left after the seventh.
Kendrick (5-4) continued his dominance of division opponents, improving to 4-1 in 11 games - four starts - this season. A day after the makeshift Mets roughed up Cole Hamels in an 11-2 rout, Kendrick pitched like one of his more accomplished staffmates.
Until the seventh, when pinch-hitter Scott Hairston hit an RBI single, Kendrick shut down New York anytime he found himself in trouble.
He gave up a leadoff double to Lucas Duda in the second but then induced three straight groundball outs. A leadoff walk in the third was quickly wiped out by a double play. He then retired nine of 10 before Ronny Paulino doubled to open the seventh.
Kendrick gave up six hits in seven innings, walking three.
Mets All-Star right fielder Carlos Beltran was out with the flu for the second straight game and manager Terry Collins again tried to take advantage of a favorable matchup with his fill-in. Hairston subbed for Beltran Saturday because of his success against Hamels and drove in five runs. This time Willie Harris got the call based on his .316 average against Kendrick.
Batting third, he had a single and a double but was stranded in scoring position each time by Bay, and walked and scored in the eighth.
Philadelphia again got the best of Pelfrey. The big right-hander began the season as the No. 1 starter in place of the injured Johan Santana but he has not been able to find any consistency.
After two solid starts in July, he gave up four runs in five innings Sunday. Pelfrey fell to 0-2 with a 9.47 ERA against the Phillies this season.
Chase Utley walked with two outs in the first, stole second and scored on Howard's hit to right field.
Kendrick and Rollins singled in the fifth ahead of Martinez. Playing for injured All-Star third baseman Placido Polanco, the switch-hitting Martinez, batting lefty, hit a drive that just cleared the angled wall in right field for a 4-0 lead.
Martinez had a sacrifice fly in the seventh for a 5-0 lead.
Booed all day, Bay came in on Howard's sinking liner and the ball hit off the top of his glove for an error to start the eighth. Beato walked three around to foul outs with pinch-hitter Ross Gload taking a free pass to push in a run. Rollins followed with his third hit scoring two needed runs.
Juan Perez relieved Kendrick and walked the only three batters he faced. Ryan Madson entered and got Duda to hit into a double play that scored a run. Paulino followed with an RBI single. Madson hit Ruben Tejada with a pitch, walked Nick Evans and gave up a run-scoring single to Angel Pagan before giving way to Antonio Bastardo, who struck out Justin Turner with the bases loaded.
While Bastardo warmed up, the Mets showed a highlight of the U.S. women's team scoring a goal against Japan in the World Cup final on the video board.
Bastardo gave up an RBI triple to Duda in the ninth but finished for his sixth save.
NOTES: The Mets left 11 on base. ... Phillies CF Shane Victorino, out since July 8 with a sprained right thumb ligament, went 3 for 5 with a double and an RBI Saturday for Double-A Reading, his first rehab game. He's eligible to come off the DL Tuesday. ... RHP Brad Lidge (right shoulder) pitched a scoreless inning for Reading in his sixth rehab appearance. He was scheduled to pitch Sunday, too. ... Mets 3B David Wright (stress fracture lower back) was expected to play his third rehab game for Class-A St. Lucie. He went 0 for 3 with a stolen base Saturday. ... Kendrick was 1 for 30 this season entering Sunday.