Webb (13-4) struck out six and allowed six hits and two walks in his first start since being chosen for the NL All-Star team for a third straight year. It was the 16th time in his 19 starts Webb lasted at least six innings.
After Webb left, Arizona's bullpen did not allow a baserunner. Chad Qualls pitched the seventh, Tony Pena the eighth and Brandon Lyon pitched the ninth for his 19th save.
Washington lost its sixth straight game.
Nationals starter Odalis Perez (2-6) was ejected in the third inning for arguing the second balk call in an inning against him.
After the call, Perez charged toward umpire Angel Hernandez, who quickly ejected Perez. The left-hander had to be restrained by manager Manny Acta, pitching coach Randy St. Claire and second base umpire Eric Cooper.
In 2 2-3 innings Perez gave up an unearned run, walked four and was called for two balks. Perez has won only two of his 16 starts this season.
It was the 11th time this season the Nationals have been shut out.
Washington loaded the bases with two outs against Webb in the fifth inning, but Webb got Austin Kearns to fly out to center to end the inning.
Perez's first balk led to the Diamondbacks' first run, moving Chris Burke
-- who reached on an error by shortstop Cristian Guzman -- to second. Burke scored on Chris Young's single.
The Diamondbacks scored their second run in the sixth inning, when Robby Hammock's single scooted past Nationals' center fielder Roger Bernadina. The two-base error allowed Mark Reynolds to score and sent Hammock to third.
Notes: The Nationals placed OF Elijah Dukes on the 15-day DL and recalled OF Kory Casto from Triple-A Columbus. ... Arizona RHP Edgar Gonzalez, on the 15-day DL with a sprained elbow, has decided against surgery, Diamondbacks manager Bob Melvin said Tuesday. ... Arizona OF Eric Byrnes, on the DL with a stained left hamstring, will have an MRI Thursday. Melvin said he may miss the rest of the season. ... Nationals RHP Chad Cordero had surgery Tuesday to clean and repair a torn labrum as well as a tendon in his right shoulder.
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