Arroyo (1-1) has pitched well so far this season, a function of being much healthier. He came down with mononucleosis during spring training last year and later developed a sore lower back, factors in the right-hander giving up a club-record 46 homers.
He gave up only two homers in his first four games, a sign of how things had changed. Now, his back is a concern again.
"Today, it felt pretty good, but it has been bugging me," Arroyo said. "I went the entire offseason trying to keep it healthy, but then it started to tighten up on me during the St. Louis start (on April 19). It was really bad two starts ago, and a little better the last time.
"It's something we're trying to keep in check, but it's hard, because you don't know what's causing it."
The Cubs hit only nine homers in April, the fewest in the majors. It was only their third multihomer game of the season.
Chicago starter Jeff Samardzija (3-1) didn't have any problems on a humid, 87-degree evening that was to his liking. He allowed only three over 7 2/3 innings, his fastball still regularly hitting 96 mph in his final inning.
Samardzija spent most of his first four seasons in the Cubs bullpen. He won a spot in the rotation during spring training and has pitched well enough to keep it.
Samardzija contained Jay Bruce, holding the NL's player of the week to a harmless double. Carlos Marmol retired all three batters in the ninth for his second save in four chances, finishing off the combined three-hitter.
The Cubs have had only six save opportunities this season, underscoring their early struggles.
It was the second straight impressive start for Samardzija, who struck out a career-high nine Cardinals in 6 2/3 innings on May 24. He's made 10 career starts in the majors.
"He usually doesn't have that command or control," Reds manager Dusty Baker said. "He was throwing 95-98 at the start and he was still at 95-96 when he left. Tonight wasn't us, it was him."
Bruce went 10 for 21 last week with homers in four straight games. He needed a homer on Wednesday to tie the club record -- Ted Kluszewski, Johnny Bench, Ken Griffey Jr. and Adam Dunn all homered in five straight.
Bruce flied out, grounded out and doubled.
LaHair led off the second inning with his sixth of the season off Arroyo, who pitched with mononucleosis and a sore lower back last year. He's been better so far, giving up only two homers in his four previous starts.
Baker said before the game that Arroyo has been bothered by a sore lower back again. Arroyo got an extra day to rest when the series opener on Tuesday night was postponed because of rain.
Stewart homered in the fourth inning, matching the Cubs' season high for homers in one game. They put together three singles for another run in the sixth off Arroyo, the run scoring on Geovany Soto's hit. Arroyo gave up nine hits and a walk in six innings, throwing 99 pitches.
The final game of the series will feature two starting pitchers celebrating their birthdays. The Cubs plan to activate RH Ryan Dempster from the 15-day DL, where he's been letting his strained right thigh heal. Dempster turns 35 on Thursday. Cincinnati will start Homer Bailey, who turns 26. ... Tuesday's rainout will likely be made up as part of a doubleheader on Saturday, Aug. 18 during the Cubs' only other visit. ... Arroyo picked Starlin Castro off second base in the first inning. ... Cubs 2B Blake DeWitt made a diving stop and flip to second base to start a slick double play in the fifth. ... The Reds signed former Cubs and A's reliever Michael Wuertz to a minor league deal. He's working out at the team's spring training complex in Arizona.