Jesus Flores homered and drove in three runs against his former club, Austin Kearns also teed off on an ineffective Oliver Perez and the Nationals improved the majors' worst record to 4-13 by snapping a three-game skid.
One of baseball's top prospects, the 22-year-old Zimmermann (2-0) beat Atlanta 3-2 in his major league debut last Monday and stifled the inconsistent Mets, too. He struck out slumping David Wright three times and allowed one run with six hits in 5 1-3 innings.
Handed an 8-1 lead, Mike Hinckley, Garrett Mock and Kip Wells provided hitless relief as Washington won for the first time in nine games away from home.
Zimmermann and starter Shairon Martis, both rookies, have all four wins for the Nationals.
It was a lethargic loss for the Mets (8-10), who host first-place Florida for a three-game series beginning Monday night at Citi Field.
Before this season, Zimmermann had never been above Double-A. But despite his inexperience, he pitched with the sort of poise and grit the Mets have long sought from Perez (1-2).
After getting tagged for seven runs and nine hits in 4 1-3 innings, the erratic lefty has a 9.31 ERA. Only four starts after re-signing with New York for $36 million over three years, he could be in jeopardy of losing his spot in the rotation.
Perez has allowed 15 walks and 23 hits in 19 1-3 innings. He was booed off the field by a frustrated crowd of 40,023 — even Wright heard catcalls during an 0-for-4 day that included a run-scoring throwing error from third base.
The All-Star slugger has fanned 23 times in 70 at-bats this season, an alarming rate for a player who set a career high last year with 118 strikeouts. He has one home run and six RBIs.
Flores finished with three hits and a walk, including a two-run homer (his second of the series) in the second and an RBI single in the third.
The young catcher was snatched up by Washington when the Mets left him unprotected in the December 2006 winter meeting draft (Rule 5), a move that certainly appears to be a mistake.
Kearns' solo shot to center, estimated at 420 feet, started a four-run surge in the fifth. The ball landed on the painted black turf that serves as the batters' eye at Citi Field, and it was the first home run in the spacious new ballpark that went between the alleys.