The former Barcelona coach, who signed a three-year contract at Bayern this year after taking a break following his departure from Barcelona in 2012, emerged from the dugout to loud cheers from thousands of Bayern fans.
"I love to attack," Guardiola had told reporters on Monday and he ordered the grass to be cut short and watered before training so the pitch was quick.
Spectators, gripped by what German media have called 'Pep-mania', paid five euros each with the money going to help for the victims of the recent German floods. Thursday's training is also open for fans.
Guardiola, wearing shorts on a chilly day, was missing several players including Brazilians Dante and Luiz Gustavo and Spaniard Javi Martinez who are all on Confederations Cup duty.
Dutchman Arjen Robben and Croat Mario Mandzukic have also not returned yet and new signing Mario Gotze, who joined from rivals Borussia Dortmund, is recovering from a muscle injury.
Midfielder Bastian Schweinsteiger was rested following minor foot surgery three weeks ago but striker Mario Gomez, reportedly close to a transfer to Italy, was training with the team though his future at Bayern is in doubt.
Midfielder Toni Kroos was also back on the pitch after missing the last two months of the season with an adductor muscle injury as were several players from the reserve team.
Expectations are high for the 42-year-old Spaniard, who won 14 of 19 possible titles in his four seasons at the Spanish club and until signing with Bayern was the most sought-after coach in the sport.
Bayern last season became the first German team to win a treble of titles, including the domestic German league and cup double and the Champions League, under Jupp Heynckes.
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