While Flores hit a grand slam, Perez contended with the aftermath of a root canal earlier in the day to pitch into the seventh inning in the Nationals' 6-4 win over the San Diego Padres on Wednesday night.
Flores drove a high fastball off Shawn Estes (1-1) into the left-field seats in the fourth inning and Washington held on to keep the Padres from assembling their first three-game winning streak this season.
Perez (2-4) was lifted after he allowed consecutive one-out doubles to Luke Carlin and pinch-hitter Tony Clark in the seventh that cut the Nationals' lead to 6-2. Scott Hairston greeted reliever Brian Sanches with a two-run home run.
The fact that Perez was even on the mound provided a big lift.
"It was tough," he said. "I couldn't sleep [Tuesday night]. It was painful. I wasn't sure if I was going to pitch."
But after sleeping just two hours, Perez got up in the morning and had a root canal on a tooth that has bothered him for the past 10 days.
"Last night we tried to call and see if they had a 24-hour dentist but we couldn't find one," Perez said. "I felt so weak. The third or fourth inning I felt bad. I threw my fastball but I had to locate it because I knew I didn't have the power to challenge those guys."
Perez was charged with three runs on six hits over 6 1-3 innings as he bounced back from a cut on his left thumb that forced him out of his last start Friday against Milwaukee.
"He did a tremendous job," Nationals manager Manny Acta said. "The guy went out there and battled for us. He gave us a great effort. He showed us a lot going out there and throwing."
The loss came before 19,201 fans, the Padres' third-smallest crowd of the season. It's no wonder: The Padres (20-34) are tied with Seattle for the worst record in the majors.
Lastings Milledge hit a solo homer for Washington off reliever Mike Adams in the sixth and Aaron Boone drove in a run with a sacrifice fly in the seventh for a 6-1 lead. Cristian Guzman had three hits.
Flores' grand slam gave Washington more runs with one swing than it has scored in eight of its last 12 games. The Nationals have scored the fourth fewest runs in the majors.
"Jesus has been playing real good baseball and showing that he belongs on this team," said Milledge of Washington's 23-year-old catcher. "He's playing good ball and I am expecting big things from him."
The Nationals beat the Padres for just the seventh time in 30 games, and only the fourth in 15 games at Petco Park.
Washington loaded the bases with one out in the fourth when Boone singled, Dmitri Young walked and Estes hit Milledge with a pitch. Estes then threw Flores a 1-2 fastball that he hit for his first career grand slam and second homer of the season.
"I had the guy 1-2 and made a really, really bad pitch," Estes said. "I was trying to get a double play and left a fastball up in a spot where he could barrel it."
Estes allowed four runs on four hits in five innings. The left-hander struck out three, walked two and hit a batter. Estes, who missed most of the last two seasons after undergoing reconstructive elbow surgery, lost for the first time since April 5, 2006.
Nationals 3B Ryan Zimmerman missed his third straight game because of a sore left shoulder. ... Padres LF Justin Huber came out of the game after the first inning because of back spasms. ... Tadahito Iguchi, who had three hits, drove in San Diego's first run with a fifth-inning single.