After an unimpressive first-half display, Bayern roared back with Croatia striker Mario Mandzukic capitalising on a mistake in the Stuttgart defence for the first goal before setting up Thomas Müller for the second.
But having watched his team labour to a 2-0 win in Munich the week before against bottom side Greuther Fürth, Sammer said Bayern had to do more.
"We have to get into our rhythm as quickly as possible," said Sammer. "As we were against Greuther Fürth, we were good, but 'good' just won't cut it for the rest of the season."
While Sammer's comments may seem harsh after two ultimately convincing wins, Bayern have some tough games ahead at Mainz and Wolfsburg, sandwiched between a home game against Schalke 04, before they play Arsenal in the Champions League.
Coach Jupp Heynckes said he was happy with the second-half display after some harsh words during the break.
"We played much better than against Fürth," said the 67-year-old, who will step down at the end of the season to be replaced by ex-Barcelona boss Pep Guardiola.
"In the first half we lacked a bit of wit, perseverance and determination in our final pass.
"I complained in the break and we went up a gear in the second half when Stuttgart started making errors."
Having won all eight of their opening league games, Bayern set another Bundesliga record in Stuttgart for having conceded just seven goals in their first 19 matches.
Goal scorer Müller said the Bavarians needed to learn to be patient against defence-minded teams eager to contain Bayern's star-studded attack.
"We need to get used to not always leading 3-0 at half-time, a football match lasts longer and we need to be patient," he said. "We punished their mistakes by going 2-0 up."
Stuttgart saw Austria striker Martin Harnik sent off for the last 10 minutes for a second yellow card after his frustration got the better of him and he clattered into Franck Ribery's ankle after the ball had gone.
"Of course, Bayern had more ball possession and dominated," said Stuttgart's Christian Gentner.
"We made simple mistakes at crucial moments, which are punished when you play Bayern Munich."