The loss snapped Washington's seven-game winning streak, and it marked the 20th time the Nationals were shut out this season.
Left-hander John Lannan started for Washington and had another quality outing, going six innings and giving up two runs on five hits. It was the top of the third that proved to be his undoing.
With two outs, Lannan had a tough time getting that final out. On a 3-1 pitch, Jimmy Rollins drove in Carlos Ruiz with a single to left and advanced to second on the throw from Willie Harris.
Chase Utley followed and was behind in the count 0-2, but Lannan couldn't put him away as Utley singled to left-center to score Rollins.
"I had to make better pitchers to Utley right there, just the way we play him right there," Lannan said. "Besides that, I felt good."
After Jayson Werth singled to put runners on first and third, Lannan tried to pick off Werth. As Lannan threw the ball to first baseman Ronnie Belliard, Utley tried to steal home. Utley crashed into Flores shoulder first at the plate and was tagged out.
Flores tried to get up and went down to the ground in pain. Manager Manny Acta, head athletic trainer Lee Kuntz and assistant athletic trainer Michael McGowan came to Flores' aid.
Flores stayed on the field for about 10 minutes before the ambulance came and transported him to the Nationals' clubhouse, where X-rays were taken. It turned out that Flores has a left ankle sprain. The X-rays found no obvious fracture, but an MRI will be taken Wednesday.
Everyone on the Nationals, from Acta to bench coach Pat Corrales, Flores' mentor, thought Utley did nothing wrong on the play. Flores got hurt because his left cleat got caught on the ground.
"When I saw that type of pain that he was in, I was very worried and really felt bad for the kid," Acta said. "The good news is that the X-rays didn't show anything. I'm optimistic that this thing will go away in 10 to 12 days. We looked at the video several times. He was right in front of the plate and he fell hard. Utley was trying to get the ball out of his glove."
The Phillies added two more runs off Levale Speigner in the top of the seventh to make it 4-0.
If there was any positive news in this game for Washington, it was that left-hander Michael Hinckley made his Major League debut and tossed 1 2/3 scoreless innings. He came in for Speigner and prevented Philadelphia from further adding to its lead. Hinckley induced Utley to hit into a double play.
"It couldn't have gone any better," Hinckley said. "After I threw that first warmup pitch, everything kind of calmed down. I just needed to remember to breath. Once I took a deep breath, I went from there and focused on the ball. I really didn't have any other thoughts, but get this guy out."
Hamels lasted 7 1/3 innings and gave up just five hits. The Nationals' best chance to score against Hamels came in the second. They had runners on second and third and no outs, but Flores hit a fly ball to center fielder Shane Victorino, who made a sliding catch and was able to double up Elijah Dukes at second.
"Dukes knows he did wrong. There is no outs and you have a runner in front of you," Acta said. "You have to make sure that the ball drops down. Still, if it's a clean single, most of the time, the third-base coach will not send you home with no outs.
"It was a great play by Victorino. The [young guys on the Nationals] are learning up here. Hopefully, it will not happen again."
Acta acknowledged that the Flores' injury knocked the wind out of the club's sails. In the dugout, the players were subdued.
"Flores is so well liked and has played so well for us, Acta said. "He has been such a big part of our offense and defense."
Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.