Guardiola arrived at the Allianz Arena in the summer after former manager Jupp Heynckes had won the Bundesliga, German Cup and Champions League.
Mourinho's relationship with Guardiola has been fractious ever since the two managed Real Madrid and Barcelona respectively, and tensions rose dramatically when Mourinho gouged the eye of the Barcelona assistant manager Tito Vilanova in 2011.
"It was Jupp Heynckes's Bayern that was the best team in Europe," the 50 year-old Portuguese was quoted as saying by Bild am Sonntag.
"Now they have a new coach and new players - and I'm not sure if they are still as good."
The two sides will face each other at the Stadion Eden in Prague on Friday night.