The Nationals insisted Strasburg wasn't trying to hit Simmons, but instead was unable to regain his control after walking Jordan Schafer on four pitches to open the second.
"He's still kind of learning to deal with the adversities of pitching up here," said Nationals manager Davey Johnson, who also was ejected by plate umpire Marvin Hudson when he argued in defense of Strasburg.
"When he went back out in the second inning, I've never seen his command so bad," Johnson said. "He couldn't come close to the first hitter he faced. Then he threw a curve ball that was eight feet outside and then a couple balls that were behind the hitter. It didn't look like he was trying to hit (Simmons). He couldn't find the strike zone."
Entering the game, Strasburg had thrown three wild pitches in 146 1/3 innings. He doubled that total by unleashing three consecutive wild pitches, including the two behind Simmons' back.
When Johnson and Strasburg were in the clubhouse after being tossed, Johnson said he immediately sought to find out if his ace was hurt.
"The first thing I said when we were both in here was 'Are you hurt? Is something wrong with you?' " Johnson said. "He said 'No. I'm just out of sorts.' "
The Nationals loaded the bases and scored two runs in each of the first two innings. On a night when the game-time temperature was 66 degrees, Strasburg said he "just got a little cold. I was just missing spots."
Asked if it was a mechanical problem, Strasburg said "I can't really explain it. I just didn't really feel good out there and couldn't hit the spot."
Braves manager Fredi Gonzalez said it was "just weird" to see Strasburg's suddenly unable to throw strikes. He said he didn't think Strasburg was trying to hit Simmons.
"I don't know if there's something wrong with him physically, because it just didn't look right," Gonzalez said. "It didn't look right."
LaRoche lifted a high fly ball into the right-field seats for this 18th homer off Kris Medlen (10-11), who was pressed into service after Atlanta exhausted its bullpen.
The game lasted 5 hours, 29 minutes.
Jason Heyward hit two homers, including a two-run shot in the ninth as Soriano blew a 7-5 lead.
Haren said he threw 30 to 35 pitches in his regular bullpen session before the game, but didn't hesitate to volunteer for the rare relief appearance.
"We needed a game like this," Haren said.
Each team used all its relievers.
Medlen, scheduled to start Tuesday at the Mets, made his first relief appearance of the season as Atlanta's ninth pitcher of the night.
Soriano suffered his sixth blown save. Heyward's second homer of the game, a two-run shot to right-center with two outs in the ninth, sent the game to extra innings.
Braves pitchers hit Bryce Harper with two pitches in Atlanta's win on Friday night, leaving the outfielder bruised and unable to start on Saturday night.
That set the stage for Strasburg.
Strasburg hit Upton in the first inning one pitch after Heyward's leadoff home run. The pitch hit Upton's backside, and he quickly ran to first.
Asked if he meant to hit Upton, Strasburg said "I'm not going to get into that."
But the answer seemed clear.
"Well after somebody goes deep and you hit him in the rear end, I don't think it's a big deal," Johnson said. "I don't know if he did it on purpose or not."
The second-inning meltdown by Strasburg was more difficult to figure out.
The drama left Braves fans howling, but no players emerged from either dugout. There were no additional incidents in the game.
There were tensions between the teams that carried over from the Braves' three-game sweep at Washington on Aug. 5-7. Both benches emptied when Harper was hit by a Julio Teheran pitch in the second game of the series.
Tanner Roark dominated the Braves after taking over for Strasburg. Roark allowed only one hit in four scoreless innings. He had a run-scoring double in the fifth for his first major league hit and RBI.
Mike Minor allowed four runs in only 1 2/3 innings, the shortest of his 78 career starts.
Harper was in Johnson's original lineup, but was held out with bruised triceps until entering the game as a defensive replacement in the ninth.
Strasburg gave up two runs and two hits, two walks and one hit batter in one-plus inning. Like Minor, he also had the shortest start of his career.
Werth doubled off Luis Ayala in the sixth and scored on a single by Ramos.
Washington's Scott Hairston was ejected by Hudson in the ninth for arguing a called third strike. ... The Nationals placed RHP Taylor Jordan on the 15-day DL with a lower back strain. Tyler Moore was recalled from Triple-A Syracuse and had two hits while starting at first base. ... The Braves signed IF Tyler Greene to a minor league contract. Greene, released by the Chicago White Sox on Tuesday, was assigned to Triple-A Gwinnett. ... 2B Dan Uggla, who had corrective eye surgery on Friday, said a test Saturday showed his vision at 20-15. He expects to be ready to play when eligible to come off the 15-day DL on Aug. 28. ... The series concludes on Sunday when Nationals LHP Gio Gonzalez faces Atlanta's Julio Teheran.