Scherzer pitched a complete game and Washington took advantage of the sloppy Cubs in a 10-3 victory in the opener of a doubleheader.
Scherzer, bidding for a third straight NL Cy Young Award, allowed nine hits. He struck out 11 without a walk and hit a batter while improving to 17-6.
''I knew he was fresh going into the ninth inning. He looked good. ... He just told me he could pitch Game 2, but I told him we'll get it,'' manager Dave Martinez joked afterward.
Scherzer also had an RBI single, raising his average to .270 this season. It was one of just six hits by Washington, which capitalized on nine walks and three errors from the Cubs. The Nationals scored five runs in the sixth inning on just two hits thanks to two errors and a wild pitch that resulted in a run.
Martinez visited Scherzer on the mound after the Cubs scored twice in the ninth, but left Scherzer in to get the final two outs.
''He asked me what I wanted to do. I said I wanted to finish it,'' Scherzer said, noting the 66-degree gametime temperature had him feeling good. ''We've been playing some hot games and for the weather to cool off, you just felt like you had unlimited energy and for me, I still had plenty in the tank.''
The right-hander retired 15 in a row after Tommy La Stella's first-inning double. He lost his shutout in the seventh.
It was Scherzer's second complete game of the season and 10th of his career.
After Friday night's game was rained out, the start of Saturday's first game was delayed 2 hours, 10 minutes by rain.
Juan Soto and Trea Turner drove in two runs each for Washington, which had lost three straight.
Victor Caratini had two hits for Chicago.
Top prospect Victor Robles, rookie-of-the-year candidate Soto and Bryce Harper started together in the Washington outfield for the first time.
Cubs manager Joe Maddon countered Scherzer with a bullpen game, and the Nationals jumped in front early. Jaime Garcia (3-7), in his Cubs debut, walked the bases loaded with one out in the first inning and Soto sent a hard grounder past first baseman Anthony Rizzo that was ruled a two-run single. That was all for Garcia, and Washington's Matt Wieters provided a third run with an RBI single off former Nationals reliever Brandon Kintzler.
Maddon wasn't thrilled with the handling of Friday's rain.
''Played when we shouldn't have, and then did not play when we should have,'' he said.
After an 81-minute delay, the teams played into the top of the second inning before the lightning and rain returned. Then after a nearly 3-hour delay - with the rain stopped - the game was finally called, necessitating Saturday's doubleheader.
The Nationals held a ceremony on the field between games placing outfielder Jayson Werth in their stadium Ring of Honor. Signed to a seven-year free agent contract after the 2010 season, Werth hit .263 with 109 homers and 393 RBIs and served as a leader. The Nationals, who had not made the postseason prior to his arrival, won four NL East titles during his time with the team. Werth threw out the ceremonial first pitch before Game 2, with his son catching.
Cubs: RF Ben Zobrist returned after being out of Friday's lineup due to neck stiffness.
Chicago LHP Cole Hamels faces Washington RHP Jefry Rodriguez in the nightcap, and then Cubs LHP Mike Montgomery opposes Nationals RHP Erick Fedde in Sunday's series finale.
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