The Bundesliga champions had endured a disappointing spell after retaining their title on March 25, taking just one point from their three league games.
And Guardiola's side looked set for another day of frustration at rock-bottom Braunschweig, as the hosts kept them at bay for 75 minutes before Claudio Pizarro finally broke the deadlock.
Mario Mandzukic then netted his 18th Bundesliga goal of the season four minutes from time to seal a comfortable Bayern win.
However, ahead of his team's trip to Madrid for the first leg of their UEFA Champions League semi-final on Wednesday, Guardiola insisted they need to raise their game if they are to beat Real.
"It has not been easy for us after winning the league," the Spaniard said. "But today we have struggled despite the difficult situation (of Braunschweig battling relegation).
"Braunschweig has played with a lot of heart and passion which is the reason why it has not been easy.
"In the second half we controlled the game more. We have won and are satisfied.
"(But) we will not get to the final of the Champions League if we do not show an outstanding performance against Real Madrid."
