A late goal from Jan Kirchhoff gave a more emphatic feel to the result after Thomas Muller and Toni Kroos netted for last season's treble-winners in the first half of their first serious test of pre-season.
It may have been Bayern's fourth win out of four since Guardiola took over, but the level of the opponents is rising and the coach admits his side's level must also increase.
"It was our first serious opponent and it was good, but I know it's going to be hard at the beginning," he said on his club's website.
"We still need time. Some important players are still injured. Our system is not the most important thing."
With Bastian Schweinsteiger injured and both Luiz Gustavo and Javi Martinez still on holiday after the Confederations Cup, Guardiola played Pierre Hojbjerg in the holding role in midfield with the rest of the side similar to the one which lifted the Champions League in May.
The surroundings in Trentino are also similar to a year ago and club chairman Karl-Heinz Rummenigge hopes that augurs well for 2013/14.
"Pep is totally satisfied," he said. "Bayern always feel at home in Trentino.
"This is where we laid great foundations for the treble last season and it's important to come back to such a place."