The hard-fought victory, combined with the 66-15 first leg win in Apia, confirmed a 108-43 aggregate win and a place in Pool A alongside Ireland, Scotland, Japan and Russia.
Germany were leading the second leg 28-21 with 10 minutes remaining, but Samoa showed their dominance to run away with another convincing win.
The Samoans have played at the last seven Rugby World Cups, and their best result was the quarterfinals at their first two in 1991 and 1995.
It is not all over for Germany who will now compete in the four-team repecharge in November in Marseille.
