Arroyo pitched six innings and allowed three runs to qualify for the quality outing. He was also tapped for nine hits with one walk and three strikeouts. What hurt most were the mistakes that caused two home runs.
Over his 7 2/3 innings, Samardzija surrendered one run on only three hits with two walks and seven strikeouts.
"That was a tough one there because we were in the ballgame, but we just couldn't get anything going," Baker said.
Leading off the top of the second, Bryan LaHair hit a 2-2 fastball up and over the plate to right-center field for a homer. A two-out homer on the first pitch by Ian Stewart in the fourth gave Chicago a 2-0 lead.
Entering the night, the Cubs' nine homers as a team were fewest in the Majors. Arroyo had only allowed two over his previous four games.
"I was trying to get in on LaHair a little bit," Arroyo said. "We thought he was diving. I just didn't get it in there. The other one was an 0-0 sinker away that wound up being up in the zone a little bit."
Samardzija was dealing early and threw first-pitch strikes to all but three of the first 14 he faced. He retired 10 of the first 11 batters with his only baserunner, Joey Votto, reaching on a wild pitch after he had struck out in the first inning.
"When you've got a devastating split, when it's on and you can get ahead of hitters, it's a huge pitch to have, but you have to get ahead of hitters to use it," Cubs manager Dale Sveum said.
The Reds didn't notch their first hit until the fourth inning. After a Votto walk, Brandon Phillips singled to center field to put runners on the corners with one out. Jay Bruce then grounded to first base, where LaHair touched the bag. Votto scored the lone Cincinnati run as Phillips forced a rundown between first and second base.
Arroyo gave the run back during a three-hit sixth inning. Following Blake DeWitt's two-out single, Geovany Soto ripped a hard RBI single to left field that scored Alfonso Soriano for a two-run Reds deficit.
"The third one, I thought, hurt quite a bit because Samardzija was throwing so good," Arroyo said. "To give him that extra breathing room makes it tough when a guy is locked in like that."
Samardzija went on to retire 11 of his final 14 batters, with a Bruce double to center field in the seventh serving as the only extra-base hit allowed. Samardzija threw 94 pitches, including 60 for strikes.
"That's the best we've seen probably this year against us," Baker said of Samardzija. "Usually he doesn't have that kind of command and control. Our reports say he's throwing the ball good, and you could see he was at 95-98, and when he left, he was throwing 95-96."
"If you pitch six innings and only get one at-bat, that means the other guy is doing his job on the other side," Arroyo said. "They deserved to win tonight."
Cincinnati did not notch a hit vs. the Cubs' bullpen, and struggling closer Carlos Marmol earned his second save with a perfect ninth. The Reds dropped to a game below .500 at 11-12.
"We can't say a whole bunch about that game," Baker said. "We didn't do anything wrong. They just did a lot of things right."
Now 1-1 with a 3.03 ERA, Arroyo came in believing he benefited from the extra day of rest provided by Tuesday's rainout. Despite his stretch of recent solid outings, he had been bothered by sore back -- an issue that plagued him at times in 2011.
"Today was pretty good but it's been bugging me," Arroyo said. "I went the entire offseason trying to keep that thing healthy. It's been really good until just before the St. Louis start [on April 19]. It tightened up a little bit during the St. Louis start. It was really bad the last time out. It was better today with the extra day of rest. It's something I've got to try to keep in check, which is tough because I don't know exactly what the cause is."