Two goals each from Bas Dost and Kevin de Bruyne gave Wolfsburg a resounding win as the Bundesliga returned after the winter break on an emotional night at the Volkswagen Arena, which saw a pre-match tribute to Junior Malanda, the Vfl youngster who died in a car accident.
Bayern conceded as many goals on the night as they did in the entire first half of the Bundesliga campaign, while Wolfsburg enjoyed more attempts on the champions' goal than any other side has managed this term.
And Guardiola conceded his side could not cope with the ruthless speed of Dieter Hecking's attacking system.
"They got an early goal and we couldn't control their counter in the first half," he was quoted as saying by the official Bundesliga website.
"Congratulations to Wolfsburg, they were better at the right moments. After a six-week break, now we need match practice."
Bastian Schweinsteiger believes Bayern were made to pay for a lack of control in their own build-up play.
"We lost the order in our attacks. We can't do that against a team so strong on the counter, with players like De Bruyne," he said. "Now we have to analyse things."
Manuel Neuer, meanwhile, is adamant his side have a lot of work to do as they continue their quest for a treble.
"It's not a good restart. It's not a disaster, but we know we have a lot of work ahead of us," said the goalkeeper.
"We lost the decisive battles. The opposition were running towards me alone - it was too easy."