Joachim Low's side proved too much for Czech Republic and Norway in their Group C matches and after picking up six points they moved five points clear of Northern Ireland.
Brazil beat Ecuador in their first Qualifier but they were then held to a 1-1 draw with Colombia and that allowed Germany to replace them at the top.
European champions Portugal have climbed three places to third, just above Argentina, while Belgium are back in the top five after wins over Gibraltar and Greece.
Despite winning both their Qualifiers, Spain are still in 11th, while England have dropped to 15th. Wales have climbed above England and Italy into 13th, with the Azzurri now 17th after losing to Spain earlier this month.
Luxembourg have climbed 35 places to 101st after their unexpected 0-0 draw with France, while the Cape Verde Islands are the biggest climbers after jumping up 47 places to 67th.