Will Venable hit his sixth career leadoff home run and also doubled and singled for the Padres.
San Diego was held to three or fewer runs for the seventh straight game and fell to a major league-worst 4-13 on the road.
Suppan (2-3) labored for 97 pitches in 4 2-3 innings, giving up five runs in his fifth start for San Diego.
The 37-year-old right-hander was the 2006 NL championship series MVP for the Cardinals and was the lone pitcher on that World Series title team to win a game in each round. The St. Louis fans hadn't forgotten, giving him a warm ovation with some standing as he left the mound.
Suppan, who spent all last year in the minors, entered 2-0 with a 2.42 ERA in four career starts in St. Louis as a member of the visiting team.
Matt Holliday singled to start the fifth ahead of Beltran's first homer in 10 days. Freese's ninth of the year made it 6-3 in the seventh.
Lynn, in the rotation for injured Chris Carpenter, recovered from a three-run first. The 25-year-old righty went six innings and worked out of frequent trouble with the Padres stranding nine runners while he was on the mound.
Venable hit his third homer of the season on Lynn's second pitch. The first five Padres reached safely with Chase Headley's RBI single making it 2-0. Cameron Maybin was caught stealing for just the second time in 15 chances on a pitchout to hurt San Diego's shot at a bigger inning.
Jesus Guzman, San Diego's cleanup man with no homers, was hit by a pitch his first two times of the season in his first two at-bats.
Skip Schumaker had an RBI double and the Cardinals added RBI singles from Freese and Matt Adams to tie it in the bottom of the first. Suppan needed 54 pitches to get through two innings, escaping damage in the second after walking Schumaker and Holliday with two outs.
Notes: Venable is a career .413 hitter (26 for 63) against the Cardinals with four RBIs. ... In 30 career starts in St. Louis, all but five for the Cardinals, Suppan is 11-5 with a 3.06 ERA. ... Headley returned after missing one game with a lower back injury. ... Eric Stults makes his second start for the Padres Thursday at New York against the Mets. The lefty allowed two runs in 6 2-3 innings against the Angels with no decision in his first start. ... Jake Westbrook was 1-1 with a 1.74 ERA in two starts last year against the Phillies, the team he faces on Thursday in St. Louis. ... Holliday is 9 for 16 against Suppan with three homers and six RBIs, although he was held to a single and walk in three trips.
Link to boxscore: St. Louis 6, San Diego 3