Clean Gasoline Act of 1999 - Amends the Clean Air Act to prohibit the manufacture, sale, supply, dispensation, transport, or introduction into commerce of motor vehicle gasoline that contains a concentration of sulfur exceeding 40 parts per million per gallon of gasoline.

Provides that a person shall not be in violation of such prohibition if, during a one-year period, the person engages in such an activity with respect to gasoline that contains a sulfur concentration between 40 and 80 parts per million per gallon if the average concentration of sulfur in the gasoline during the period is less than 30 parts per million per gallon.

Requires the Administrator of the Environmental Protection Agency to report to the Congress on the effects of use of low sulfur motor vehicle gasoline on urban and regional air quality. Provides for an update within two years of submission of the original report.

Authorizes the Administrator to promulgate a regulation to establish maximum and average allowable sulfur concentrations in motor vehicle gasoline that are lower than concentrations specified under this Act if: (1) research conducted after this Act's enactment indicates that significant air quality benefits would result from a reduction in allowable sulfur concentration in such gasoline; or (2) advanced vehicle technologies have been developed that can significantly reduce emissions of air pollutants from motor vehicles but that require gasoline with a lower concentration of sulfur than that specified under this Act.

Prescribes penalties for violations of this Act.