Kendrick said he fell behind in the count too often and the result showed on the scoreboard.
"I think I just fell behind in the count [to a lot of hitters]," he said. "So when you fall behind, it's tougher to pitch [and] that's what happens."
In the first, Ryan Sweeney lined an RBI single to center to put the Cubs ahead, 1-0.
In the third, Anthony Rizzo hit a double off the wall in right to plate Starlin Castro to make it 2-0.
Kendrick allowed a leadoff single to Donnie Murphy and a Brian Bogusevic ground-rule double in the fourth before Welington Castillo hit a two-run double to left-center to make it a 4-1 game.
One out later, Darwin Barney hit a sacrifice fly to right field to plate Castillo for Chicago's fifth run. Castillo dislodged the ball from catcher Erik Kratz's glove when Kratz tried to apply the tag following a strong throw from Darin Ruf.
Kendrick, who walked one, hit a batter, and struck out four, has lost four straight decisions for the first time since June 6-28 of last season. He also lasted six innings or fewer for the ninth consecutive start.
The right-hander is 4-9 with a 5.74 ERA (58 ER in 91 innings pitched) in his last 16 starts dating back to June 8.
"The last two or three outings, it's been something a little bit different," Phillies interim manager Ryne Sandberg said. "But today, [Kendrick] just didn't have his two-seam fastball that he can throw to the front side of a left-handed hitter and he can throw to right-handed hitters and get ground balls.
"[That resulted] in 11 fly-ball outs and two ground-ball outs. With men on base, he wasn't able to get ground balls for double plays and he was pitching up at thigh level without the sink to it. So, those balls got hit in the gaps with men on base."
Meanwhile, the Phillies' offense couldn't get anything going against Cubs starter Jake Arrieta, who stymied Philadelphia hitters for 6 2/3 innings, allowing only three hits.
Ruf hit his 12th home run of the year, a solo shot to left-center, in the fourth for Philadelphia's only run of the game. It was his 10th homer in 30 games.
"A lot of our guys didn't have too much of a history with [Arrieta], so the first time through the lineup he was pretty sharp and that trend continued," Sandberg said.
"Our guys had a tough time making adjustments. He mixed it up. He had a cut fastball that was breaking about a foot at times, which is abnormal for a cut fastball. He was jamming some left-handed hitters with it and the ball was running away from right-handers."
Cubs manager Dale Sveum also emphasized the importance of Arrieta's cutter in his ability to quiet Philadelphia's bats.
"When his command is going, and he's throwing strikes, there's not a whole lot going on [for the other team]," Sveum said. " … When he's in the zone, and you have that 90 mph slider, cutter and his curveball [that] was pretty good today, when he's in the zone, he's pretty tough. When he gets command of that cutter, it'll be a pretty powerful pitch in the league."
Sandberg said he missed Michael Young's bat in the lineup Sunday. Young -- who was traded to the Dodgers Saturday night -- was 7-for-12 with three RBIs in the first two games of the series.
"The way [Young] had been going on this road trip, a bat like that could hit anywhere in the top five spots. He helped us win games on this road trip, so you miss a bat like that."
Reliever J.C. Ramirez allowed a pair of runs in the eighth, walking three batters in the frame.
The Phillies lost their first series to the Cubs since losing three out of four to Chicago from July 15-18, 2010, at Wrigley Field. Philadelphia had won four series and split one over that period.