"You have a game like today and you have a game like Friday where the pitching sort of gets away from you, it's tough to get momentum," said Padres manager Bud Black. "Obviously when you're not scoring runs consistently, it makes it tough to really get anything going. And that's sort of where we are."
After throwing an eight-inning, five-hit gem against Philadelphia in his last start, Zimmermann (5-2) picked up where he left off, striking out four of the first six batters he faced.
Alexi Amarista lofted a single into right field with one out in the sixth to break up Zimmermann's perfect game bid, but the Nationals' pitcher responded by striking out pinch-hitter Tommy Medica and Everth Cabrera.
He only allowed one more hit the rest of the way, and didn't allow any walks while recording a season-high 12 strikeouts.
"For the most part he was down in the zone, painting corner to corner," said Padres first baseman Yonder Alonso. "He commands so well, gets ahead of guys really quick. We couldn't really put any good swings on him."
Stults (2-7), meanwhile, struggled from the beginning in his first start since taking bereavement leave last week after the death of his grandmother.
Washington scored one off Stults in the first, two in the second and another in the third before he loaded the bases and was replaced by Tim Stauffer. On Stauffer's first pitch, Danny Espinosa laced a two-run single to left to make it 6-0 before the Padres even had anyone reach base.
Stults was responsible for all six runs, giving up eight hits and no walks while recording two strikeouts in 2 1/3 innings, the shortest start of his career. That put the Padres in a deep hole that would be difficult for any team to dig out of, let alone the Majors' worst scoring offense.
"Today was definitely a rough one," Stults said. "We feel like we're making some progress, but it's frustrating when you don't see the results on the field."
It was the latest disappointment for Stults, who hasn't won since May 10 and now has an ERA of 5.68. Opponents are hitting .321 off of him, and after giving up 18 home runs in more than 200 innings last year, he's served up 13 in 65 innings.
"His pitches are up in the zone. He's not locating his fastball," Black said. "A pitcher like Stultsy has to hit his spots. And today he didn't do it, and they took advantage of it."
Ian Desmond hit his second home run in as many games on a fastball down the middle for a two-run blast in the second inning that Cameron Maybin nearly pulled back into the ballpark.
"I miss over the plate when I try to go inside with some fastball to righties, and that's when I get hurt," Stults said. "Today is just one of those days where things didn't go my way."
San Diego couldn't even score after they were gifted a leadoff triple in the seventh. Seth Smith's line drive to right easily could have been ruled a single and a two-base error on Jayson Werth, who let it roll under his glove. But Carlos Quentin grounded out to third, Chase Headley popped out and Alonso lined out to center to continue the Padres' futility at the plate.
It was the 10th time the Friars have been shut out this season, while only pitching one of their own, a complete game one-hitter by Andrew Cashner on April 11 against Detroit.
Every Washington position player except for catcher Jose Lobaton had a hit Sunday.
San Diego has won just one series in its last seven tries. The defeat gave Washington the season series, four games to three.
After an off-day Monday, the Padres embark on an eight-game road trip to play the Phillies, Mets and Mariners before returning home for the second half of a four-game, away-home set against Seattle.