The World Cup winning coach picked former Barcelona coach Pep Guardiola ahead of Mourinho despite Real Madrid pipping the their arch rivals to the Spanish league title.
Del Bosque won the Champions League with Real Madrid and says no one can doubt his allegiance to Los Blancos.
"I don't have anything against Real Madrid nor Mourinho," Del Bosque told RTVE.es. "Nobody can tell me what Madridismo means because I know very well.
"I have chosen Guardiola because he's Spanish and for everything that he has done. He has won three titles this year. When I choose a coach, I do it for his sporting merits as well as his behaviour."
The 61-year-old also chose former Chelsea manager Roberto Di Matteo in his top three "because of what he did with Chelsea after coming in halfway through the season", guiding the Blues to their first ever Champions League title.
Cesare Prandelli led an unfancied Italy side to the Euro 2012 final and was Del Bosque's final nomination as he "chose to give a nod to national teams".
The winner of the award will be unveiled at the Fifa Gala in Zurich on 7th January.