The Bavarian giants looked unconvincing in the first half of Saturday's game and fell behind as Hiroshi Kiyotake gave Hannover a deserved lead in the 25th minute.
That seemingly sparked Bayern into life, though, as Xabi Alonso fired a free-kick beyond Ron-Robert Zieler, just before Guardiola withdrew Dante for Robert Lewandowski in a surprising tactical tweak.
Bayern's superiority eventually shone through as Thomas Muller netted twice in the second half, once from the penalty spot and then with a towering header, with Guardiola delighted to see his side make the most of Wolfsburg's 1-0 defeat to Augsburg by going 11 points clear.
"Hannover were superb in defence," he told reporters. "And that's why it was difficult for us.
"Wolfsburg have failed to take points so it's a good weekend for us.
"We'll take a break on Sunday, but as of Monday we'll focus on the Champions League and Shakhtar Donetsk."
Centre-back Holger Badstuber was also quick to highlight Hannover's role in making it a tricky encounter for Bayern.
"Hannover pulled everyone back and that made it hard," the defender added. "The pitch wasn't easy either.
"We couldn't move the ball as fast as we like to and we didn't establish positions between the line.
"On top of that, they scored the opening goal. We improved in the second half. It was a hard-working victory."
