Tyler Clippard escaped a jam in the eighth and Rafael Soriano rebounded in the ninth for his 13th save this season. Washington has won three in a row and nine of 11.
The Nationals stopped San Francisco's five-game winning streak with a 9-2 victory in Monday's series opener. And they continued to slow down the team with the best record in baseball by beating its hottest pitcher on a windy, chilly night in San Francisco's waterfront ballpark.
Span drove in a run with a sacrifice fly and Werth singled home another against Bumgarner in the fifth. It was all Washington needed to end Bumgarner's winning streak.
Bumgarner (8-4) allowed eight hits in seven innings. He struck out five and walked one intentionally.
The tall left-hander with the deceptive fastball was selected NL player of the month for May after going 5-0 with a 2.08 ERA. He hadn't lost since April 28 against San Diego.
It was a far better feeling for Fister than his last start in San Francisco, which came on a warm October evening in 2012. He was struck squarely in the head by Gregor Blanco's line drive in the World Series, a ball hit so hard it caromed into shallow center field, though the 6-foot-8 pitcher appeared unhurt and stayed in the game.
Every time the Giants put together a few hits in the rematch, Fister flexed his best stuff -- and so did his new club.
In the third, San Francisco put two runners on before Buster Posey struck out. Pablo Sandoval, who finished with three hits and a walk, and Michael Morse singled to start the fourth before Fister induced three consecutive flyouts.
In the sixth, Sandoval doubled and tried to score on Crawford's two-out single to right. Instead, Werth charged in to field the hard-hit ball and easily threw out the portly Sandoval at the plate.
Clippard allowed two baserunners with one out in the eighth before completing his 20th consecutive scoreless inning.
NOTES: Nationals 3B Anthony Rendon returned to the lineup after sitting out the past three games with a sore right hand. He singled twice, struck out and flied out. ... Giants RHP Santiago Casilla, on the disabled list with a strained right hamstring, is scheduled to toss one inning at Class-A San Jose on Thursday and two innings Saturday. ... Matt Cain (1-3, 3.52 ERA) starts for San Francisco against Washington's Tanner Roark (4-4, 2.91) on Wednesday night.