Carlos Beltran, who got his 1,000th RBI on his 32nd birthday, and Fernando Tatis both tripled for the Mets, who returned home for their second homestand at Citi Field and stopped a four-game losing streak.
Nick Johnson and Jesus Flores homered for the Nationals, a major league-worst 3-12. While 26 homers were hit in the first six games at the new Yankee Stadium, there have been just 12 in seven games at Citi Field, where not a single home run to center has been hit yet.
Santana (3-1) allowed one run and six hits in six innings, walked one and reached double digits in strikeouts for the 45th time in his career. Johnson's sixth-inning homer raised Santana's NL-leading ERA from 0.46 to 0.70.
New York has scored just seven runs in Santana's four starts.
"The last games that he's pitched have been somewhat stressful in the sense that every pitch meant something or every play meant something," Mets manager Jerry Manuel said before the game.
New York's offense didn't change, going 2-for-18 with runners in scoring position and stranding 13 runners.
Bobby Parnell and Pedro Feliciano escaped trouble in the seventh, J.J. Putz pitched the eighth and Francisco Rodriguez allowed a two-run homer to Flores before finishing for his fourth save in four chances.
A crowd of 40,522 was at Citi Field on a warm evening, the largest since the April 13 opener at the $800 million ballpark.
The Mets had been the only team in the majors not to face a left-handed starter before batting against Scott Olsen (0-3), who gave up three runs
- two earned - and nine hits in six innings. Right-handed-hitting Gary Sheffield was inserted into right field and Tatis into left.
New York went ahead in the third when Luis Castillo singled and Beltran tripled on a liner to center in which Elijah Dukes tried for a shoestring catch only to have the ball roll past him to the warning track. The play originally was scored a single and an error, then was changed.