Colon (14-11, 4.13) extended his streak to 31 innings before Jace Peterson's RBI triple in the seventh ended the run. Andrelton Simmons followed with an RBI single to cut the Mets' lead to 4-2, and Colon left in favor of Dario Alvarez with two out.
Colon surpassed Hall of Famers Cy Young (1909) and Warren Spahn (1963), who shared the previous record with 27 straight scoreless innings.
Colon, pitching after a long rain delay pushed the start to 9:30 p.m., allowed seven hits with two strikeouts and a walk in 6 2/3 innings.
Colon came with 1 2/3 innings of the Mets' team-record scoreless streak of 32 2/3 held by R.A. Dickey. Jerry Koosman (31 2/3) is second, and Colon, Tom Seaver and Dwight Gooden are tied for third.
Kevin Plawecki and Juan Uribe each had three RBI for the Mets, who extended their NL East lead over idle Washington to 7 1/2 games. They reduced their magic number to 16 with 22 games to play.
Colon's RBI single in the fourth followed Plawecki's two-run double off Braves starter Shelby Miller. Uribe had an RBI single in the seventh.
Plawecki drove in another run in the eighth when his fielder's choice grounder scored Eric Young Jr. Uribe had a two-run double in the ninth.
Addison Reed pitched a scoreless ninth for the Mets, allowing a hit and a walk.
Steven Matz (2-0, 1.89) faces Matt Wisler (5-6, 5.81) Friday (7:35 p.m., SNY) in the second game of the series.