Latos (3-1), a rookie, limited the Braves to six hits while walking two and striking out three in earning his third straight victory in just four career starts.
Heath Bell pitched a 1-2-3 ninth to get his 27th save.
Kyle Blanks homered and Kevin Kouzmanoff and Oscar Salazar each drove in a run for San Diego, which has won six of its last seven games.
Adam LaRoche homered and Brian McCann drove in a run for Atlanta, which lost its second straight game and its fifth out of seven.
Braves' starter Kenshin Kawakami (5-9) went six innings, allowing three runs on eight hits with no walks and four strikeouts.