First-half goals from Jerome Boateng and Franck Ribery, along with a stoppage-time penalty from substitute Thomas Muller, saw Bayern chalk up 37 league games unbeaten and surpass Hamburg's 30-year-old record.
Nevertheless, on the back of Tuesday's laboured Champions League win over Viktoria Plzen, Guardiola was disappointed by his team's drop off in intensity between the strikes from Boateng and Ribery that bookended the opening period.
"We started well, and the early goal made it easier," the Spaniard told the club's official website. "But we didn't play so well after that.
"It was better in the second half, we controlled the game and created a number of big chances.
"I hope my players come back fit after the international break."
Ribery slammed home an emphatic free-kick on the stroke of the interval and the Frenchman is relishing the top-of-the-table clash at Borussia Dortmund - 2-1 losers to Wolfsburg on Saturday - immediately after the forthcoming internationals.
"The goal was good for the team and for me," he said.
"We did well, we were aggressive and played better than we have done recently.
"The game in Dortmund is a very important one. It's a massive chance. We have to keep it up now.
"We need to keep working and winning, and extending the record."
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