Joachim Low's side have sat second behind Spain for all but one month since April 2012, but their Maracana success last Sunday puts them back to the top of the rankings for the first time since June 1994.
Beaten finalists Argentina climbed three places to sit just behind the Germans in second.
Spain had led the way in every year since the side's 2008 UEFA European Championship triumph, but they slip to eighth after a disastrous World Cup campaign that saw them exit at the group stage.
Netherlands rose 12 spots to return to the top three for the first time in two years and Costa Rica's own 12-place jump leaves them in their best position in 16th.
Colombia are fourth and Belgium round off the top five after their run to the quarter-finals also resulted in a record high position.
France (10th) are back in the top 10 for the first time since their disastrous World Cup campaign in 2010, but three of Europe's biggest sides plummeted out after poor showings in Brazil.
Portugal dropped from fourth to 11th, Italy are 14th, their lowest placing in four years, while England's group-stage exit leaves them 20th, an 18-year low.
Algeria remain Africa's top-ranked nation, although their run to the last 16 in Brazil was not enough to prevent them slipping two places to 24th.
Japan are now Asia's highest-placed outfit. They sit 45th, improving by one place, while Iran have dropped six spots to 49th - both finished bottom of their respective World Cup groups with just one point.
