Lynn (1-1) allowed one run and six hits. He pushed his April record to 13-2 since 2012, the best record in the majors over that period.
Wily Peralta (0-1) gave up four runs on 10 hits over five innings for Milwaukee.
Yadier Molina had three hits for St. Louis, which won 12 of 19 against Brewers last season.
Kevin Siegrist, Seth Maness, Matt Belisle, Randy Choate, Jordan Walden and Trevor Rosenthal followed Lynn. Rosenthal picked up his third save despite giving up a two-out run-scoring hit to Ryan Braun in the ninth.