Arjen Robben's stunning goal 27 minutes in was enough for the Bundesliga champions to claim all three points at the Olympiastadion and move them 10 points clear at the top of the table.
Bayern controlled the game in typical fashion before half-time, but were made to work hard to keep hold of their lead by a spirited Hertha display after the break.
Guardiola admitted his team were below their usual standards in the second half, and attributed their drop in intensity to the exertions of playing most of last Wednesday's UEFA Champions League defeat at Manchester City with 10 men.
The Spaniard commented: "We played well in the first half, but in the second half we lacked our style, our way of playing.
"It's always dangerous when you're only 1-0 up, and Hertha are quick on the break.
"After 70 minutes with only 10 men in Manchester my players may have been a little tired. I'm happy with the first half, but we can do better than in the second."
Match-winner Robben, meanwhile, added that the only thing that mattered for Bayern was the victory.
"Sometimes you just have to accept a 1-0 win. We can't always play top football," said the Dutchman.
"The second half wasn't good. Three points, and we move on."
