Joachim Low's men beat Argentina 1-0 after extra time in Sunday's final at the Maracana courtesy of a Mario Gotze goal in the 113th minute after previously dispatching Brazil 7-1, France 1-0 and Algeria 2-1 after extra time in the knockout stages.
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"This is amazing for Germany. I'd like to congratulate all my players and head coach Joachim Low," Guardiola told Bayern's official website.
"Enjoy this unbelievable World Cup win. Germany fully deserve it."
Bayern sporting director Matthias Sammer, meanwhile, was full of praise for the national team as the nation celebrates the triumph.
"What an amazing win. I am delighted for the German national team, for Jogi Low and for Bayern's seven world champions," he enthused.
"This is a great achievement. Our team deserved this and all of Germany is delighted with it."