Alonso made the move from Real Madrid to Bayern in August and, as well as featuring in midfield, has often formed part of a defensive line in front of Neuer.
The Germany international has cemented his position as one of the world's best goalkeepers in recent years and was rewarded with a nomination for the FIFA Ballon d'Or recently.
Having featured alongside Neuer for the last few months, Alonso revealed he has been taken aback by the goalkeeper's quality as well as that of versatile midfielder David Alaba.
"I must say that he is not only by far the best goalkeeper with whom I have ever played but also as an 11th outfield player he is outstanding," he told Sport Bild.
"Of course I already knew that he was world class but, along with David Alaba, he has nevertheless surprised me in Bavaria by how strong he really is."
Neuer will go up alongside five fellow Germans for the Ballon d'Or, with World Cup winners Philipp Lahm, Mario Gotze, Toni Kroos, Thomas Muller and Bastian Schweinsteiger also nominated.
However, Alonso believes the individual achievements of former winners Cristiano Ronaldo and Lionel Messi could make them favourites.
Asked who he felt would win the award, Alonso added: "It is the fundamental question. Counting individual or personal accomplishments? In that case, it is always difficult against Messi and Ronaldo.
"Or is it the successes with the team? Then the Germans have the best opportunities."
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