Philadelphia (83-71) dropped its fourth consecutive game. Trying for their first playoff appearance since 2011, the Phillies are just a half-game ahead of Milwaukee for the third NL wild card.
Nola (10-13) was charged with four runs - all in the fifth - and five hits in six innings. The right-hander struck out eight and walked none.
Chicago (69-86) won for the seventh time in eight games. Rookie right-hander Hayden Wesneski (3-1) pitched into the sixth inning, and Yan Gomes drove in the team's first run.
Manuel Rodriguez got two outs for his fourth save. He entered with a runner on first and retired J.T. Realmuto on a soft liner to shortstop before Alec Bohm bounced into a forceout at second.
''We had 14 baserunners,'' Phillies manager Rob Thomson said. ''We just didn't come through with big hits. We've gone into stretches like that before. We got to come out of it, and we will.
''We got to fight through it and move forward.''
Nola breezed through the first four innings, striking out five consecutive batters at one point. First baseman Rhys Hoskins made a diving stop to rob Willson Contreras of a hit for the second out of the fourth.
But Nico Hoerner opened the fifth with a leadoff single. He stole second and advanced to third on Patrick Wisdom's single before coming home on a fielder's choice by Gomes.
Alfonso Rivas then was hit by a pitch ahead of Morel's 16th homer, a drive to left field. He also went deep in Chicago's 2-1 victory on Tuesday.
Morel is one of three rookies in franchise history to hit 15 or more home runs and steal 10-plus bases in a single season, joining Billy Cowan (1964) and Kris Bryant (2015).
Nola had allowed only one homer in his previous 25 2/3 innings prior to Morel's shot.
Wesneski (3-1), auditioning for a spot in the 2023 rotation, allowed one run and six hits in five-plus innings. He stranded runners in scoring position in the second, fourth and fifth.
Kyle Schwarber used his legs to manufacture the Phillies' lone run off Wesneski in the third. With Bryce Harper at the plate, Schwarber took advantage of the Cubs' shift to take a walking lead and steal an unoccupied third base before Wesneski could deliver a pitch.
Harper followed with a sacrifice fly that gave the Phillies a lead that stood until the fifth.
Wesneski was pulled after Nick Castellanos opened the sixth with a single, but Mark Leiter Jr. retired the next three batters.
Wesneski has a 1.96 ERA with 16 strikeouts in 18 1/3 innings covering three starts, and he has a 2.33 ERA in five appearances since being promoted from Triple-A Iowa on Sept. 6. He was acquired in a trade with the New York Yankees in August.
''Even when he's not in cruise control, it feels like he has control of the game,'' Chicago manager David Ross said. ''He did a really nice job of continuing to work through a tough, deep lineup and made pitches when he had to.''
The Phillies cut the deficit to 4-2 in the seventh when Schwarber doubled, advanced to third on a bloop single by Hoskins and scored on Harper's grounder to second.
But Adbert Alzolay relieved Leiter and retired Realmuto on a liner to second and struck out Bohm.
PHILLIES WAITING ON WEATHER
Thomson said the Phillies still plan to travel to Washington following Thursday's game against the Cubs. The Phillies are scheduled to play a four-game series against the Nationals that includes a doubleheader Saturday that could be affected by potential weather issues caused by Hurricane Ian.
SUZUKI EYES RETURN TO NORMALCY
Cubs right fielder Seiya Suzuki believed it was important to return from his native Japan to finish the season after attending to the birth of his first child last weekend.
''Numbers-wise, I'm not satisfied and feel I can do better,'' said Suzuki, who is batting .263 with 13 homers and 45 RBIs in 103 games in his first season with the Cubs. ''I think the most important thing is I'm getting used to life here, and that's going to be a benefit next year.''
Suzuki returned with his hair dyed blonde.
''The baby keeps crying all night, so it's all the stress,'' Suzuki joked through a translator.
Cubs: LHP Justin Steele (low back strain) will throw one more ''intense bullpen,'' Ross said. But Ross isn't sure if he will pitch again this season. ... LHP Drew Smyly (shoulder stiffness) will make a start before the end of the season, Ross said.
The Phillies will start LHP Ranger Suarez (10-5, 3.38 ERA) in Thursday's series finale against the Cubs. Javier Assad (1-2, 4.28 ERA) takes the mound for Chicago.
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