Bryce Harper also connected for the Nationals, who reduced their magic number to three. They have a four-game lead over Atlanta with six to play.
Gonzalez (21-8) settled down after a shaky start and lasted six innings, allowing three runs and six hits. He's the first NL lefty to win more than 20 games since Dontrelle Willis won 22 for the Florida Marlins in 2005.
Gonzalez and Mets knuckleballer R.A. Dickey (20-6) are considered the leading candidates for the NL Cy Young Award.
The Phillies closed out their home schedule with a loss that left them on the brink of postseason elimination. They trail St. Louis by six games for the second wild-card spot with six games remaining. They finished 40-41 at home, their first losing record at 9-year-old Citizens Bank Park.
The Nationals already are the first major league team in the nation's capital to reach the postseason in 79 years. They're looking for their first division crown since moving to Washington and the second in franchise history. The Montreal Expos won the NL East in 1981, a strike-shortened season.
Tyler Cloyd (2-2) got roughed up by an offense that feasted on his straight fastballs. Cloyd, who was 15-1 in the minors this season, allowed six runs and six hits in five-plus innings.
Cloyd walked Danny Espinosa to start the fifth and Jayson Werth with two outs. Harper then hit a soft liner to left for a single, scoring Espinosa for a 4-3 lead.
Morse crushed a two-run shot to right-center to give the Nationals a 6-3 lead in the sixth. The ball sailed over Philadelphia's bullpen and landed in front of Washington's relievers, traveling an estimated 448 feet.
Harper ripped one out to right-center to give the Nationals a 1-0 lead in the first. He also homered in his first at-bat Wednesday to become the second teenager to hit 20 homers, joining Tony Conigliaro.
Darin Ruf lined a three-run double over Harper's head to put the Phillies up 3-1 in the first.
Ruf earned the nickname "Babe" by leading all minor leaguers with 38 homers this season, breaking Ryan Howard's single-season record at Double-A Reading. He hit his first homer Tuesday in his third at-bat and first start.
Morse connected in the second to cut it to 3-2.
The Phillies acquired Gonzalez from the Chicago White Sox along with Aaron Rowand and another minor leaguer in 2005. They traded him back to the White Sox with Gavin Floyd for Freddy Garcia in 2006 in what turned out to be the worst trade by Hall of Famer Pat Gillick in his three years as Phillies general manager.
Gonzalez has won at least 15 games three straight years and is a two-time All-Star. Floyd has won double-digit games five consecutive seasons. Garcia won one game for Philadelphia.
NOTES: Morse became the sixth player to hit 15 homers for the Nationals, most in franchise history. It was his second multihomer game of the season and fifth of his career. ... Harper is three homers shy of matching Conigliaro, who hit 24 for the Boston Red Sox in 1964. ... The Phillies lead the majors in attendance at 3,565,718. ... Cliff Lee (6-8) faces Mark Buehrle (13-13) when the Phillies start a three-game series at Miami on Friday night. ... Edwin Jackson (9-10) tries to become the fifth Washington starter to win 10 games when the Nationals visit St. Louis on Friday.