Clean Vehicles Incentive Act of 2013 - Amends the Internal Revenue Code to allow certain businesses located in areas designated as nonattainment areas under the Clean Air Act a general business tax credit for the cost of certain clean-fuel vehicle property and the use of clean-burning fuel. Allows the credit to be taken against regular and alternative minimum tax liabilities. Allows a tax deduction for any unused clean fuel credit amounts.

Allows a new qualified hybrid motor vehicle tax credit for any taxable year after 2012 only for such a vehicle which is placed in service after December 31, 2012, by an eligible business and substantially all of the use of which is in a nonattainment area.