The Nationals have won four straight games and improved their record to 42-70.
It looked like it was going to be a long night for the Nationals after Tim Redding gave up three runs in the first inning. But Washington would take the lead by the third inning off Colorado right-hander Aaron Cook.
In the third, Flores hit his eighth home run of the season, a solo shot over the left-field wall. The next inning saw the Nationals score four more runs, thanks to errors by Cook and shortstop Troy Tulowitzki. With runners on first and second and no outs, Willie Harris bunted the ball to Cook, who threw the ball away as he tried to force Redding out at third base. Redding and Bonifacio both scored.
Later in the inning, with the bases loaded, Harris and Lastings Milledge scored when Tulowitzki threw the ball away as he was trying to turn a double play on a ball hit by Flores.
In the sixth, Bonifacio and Harris had RBI hits, while Harris hit a two-run homer in the top of the eighth off Matt Herges.
"Bonifacio continues to be a spark -- offensively and defensively," manager Manny Acta said. "He puts a lot of pressure on the other teams when he is on base. Flores continues to be a big RBI guy for us. Even when we were not doing good, Willie Harris was our bright spot and he continues to play well for us. "
Cook ended up pitching 5 2/3 innings and gave up seven runs -- four earned -- on 11 hits.
"It's the first time -- with any team I've been associated with -- that we've scored five runs off Aaron, because he is so tough," Acta said. "We caught a couple of breaks with the errors, but we did have some good at-bats against him, too."
In the past, if the Nationals were down by three runs, there was a good chance that they would not come back and win the game. But the acquisitions of Bonifacio and Alberto Gonzalez have made a difference on the field.
"We are playing better defense. We played four clean ballgames," Acta said. "We have more energy with these young guys out there and it's rubbing off [on the rest of the players]. We're trying to get back to playing fundamental baseball and defense, which hurt us in the month of July."
Bonifacio is modest when he talks about the contributions that he and Gonzalez have made to the team in the last four days.
"I don't want to say that we are winning because we are here. We are just playing good baseball," Bonifacio said.
Redding ended up with the victory as he pitched five-plus innings and gave up four runs on six hits. He acknowledged that he didn't feel right warming up before the game and in the first inning.
Starting with the third inning, however, Redding retired nine straight hitters. He would leave the game after giving up a single to Garrett Atkins and walking Ian Stewart in the sixth inning.
"The shoulder was a little tight. I never felt I couldn't get loosened up," Redding said. "So the first inning, I was going out there and seeing what I could do. I was trying to loosen up. At the same time, I was trying to make pitches. As you saw, I missed my spots a few times."
Rockies manager Clint Hurdle came away impressed with Redding.
"His location was better," Hurdle said about Redding. "He has more of a fastball than you think. Obviously, he's got a good breaking pitch. He's had success for a reason. He kept the ball out of the middle of the plate with a lot better regularity after that inning. He probably still threw a lot more pitches than he wanted to, but it shows why he's won more games than he's lost."
Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.