The Reds picked on Adam Wainwright (0-3), a 20-game winner in 2010 coming off reconstructive elbow surgery that sidelined him all of 2011.
Wainwright is winless in his first three decisions for the first time in his career. He allowed multiple home runs in consecutive starts for just the second time ever.
Wainwright allowed four runs in five innings, leaving him with a 9.88 ERA.
Phillips hit his first homer and Ludwick hit his second in a span of three at-bats in the third inning. Stubbs, who was 3 for 5, hit his first off Victor Marte in the seventh.
Matt Holliday's three-run homer in the sixth was the only damage against Arroyo (1-0), who struck out five and walked none while scattering five hits. Arroyo threw just 90 pitches.
Cardinals center fielder Jon Jay left after the seventh with a sprained right shoulder, likely from bumping into the wall trying to snare Stubbs' homer. Earlier Thursday, general manager John Mozeliak said first baseman Lance Berkman likely would be placed on the 15-day disabled list with a left calf injury.
Phillips got his first RBI with one out in the third, Jay Bruce followed with a single and Ludwick hit the next pitch beyond the visitor's bullpen.
Arroyo allowed two hits the first five innings, but the Cardinals opened the sixth with three straight hits. Rafael Furcal and Jay singled before Holliday, who had been 3 for 26 on the homestand, hit his third homer to cut the deficit to 4-3.
The NL Central-leading Cardinals are 9-4. A sweep over the Reds would have given the franchise its best start to the season since it was 13-3 in 1982, a World Series title year.
NOTES: The Reds are 3-21-2 in 26 series in St. Louis since the start of 2003. ... RHP Homer Bailey (0-2, 5.40) starts for the Reds in the opener of a three-game series at Chicago on Friday. St. Louis' Lance Lynn (2-0, 1.50) makes his fifth career start at Pittsburgh. ... Wainwright previous allowed homers in consecutive starts May 5 and 10, 2009, surrendering two each against the Phillies at home and at Cincinnati. ... Marshall has seven strikeouts in 4 1-3 innings.
Link to boxscore: Cincinnati 6, St. Louis 3