Some are being reduced to levels before the city instituted a letter grade system in 2010.
Under the agreement, 60 percent of all violations will result in the minimum $200 fine.
Previously, fines were up to the discretion of a hearing officer. In some cases, that resulted in fines as high as $2,000 for minor offenses.
The changes will reduce total fines collected by more than $10 million a year.
Quinn is also backing legislation that would allow restaurant owners to request an inspection consultation to help identify problems before they are graded.