Reds starter Johnny Cueto (15-7) was off-kilter from the get-go and missed a chance to become the majors' first 16-game winner. He allowed five runs in five-plus innings.
The Cardinals have won eight of nine and swept the Reds at home for the first time since Sept. 26-28, 2008. Cincinnati has lost 10 of 12, with Cueto getting the two wins.
Jon Jay had three hits, scored twice and was plunked by a pitch for the sixth time in six games for St. Louis.
Lynn (14-8) gave up four singles and was set to pitch the eighth leading 5-0 before a 58-minute rain delay ended his outing.
Trevor Rosenthal got two outs for his 37th save in 42 chances.
