Medicare Drug Savings Act of 2013 - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act (SSA) to require drug manufacturers to pay the Secretary of Health and Human Services (HHS) drug rebates for rebate eligible (low-income) individuals. Excludes from Medicare coverage as a part D drug any drug or biological manufactured by a manufacturer that has not entered into and have in effect a rebate agreement with the Secretary.

Requires a rebate agreement to require a drug or biological manufacturer to provide to the Secretary a rebate, determined according to a specified formula, for each rebate period ending after December 31, 2011, for any covered Medicare part D drug dispensed after that date to any rebate eligible individual for which payment was made by a prescription drug plan (PDP) sponsor or MedicareAdvantage (MA) organization for such period.

Specifies a formula for determination of Medicaid rebate amounts for such drugs or biologicals.

Amends SSA title XIX (Medicaid) to exclude any amounts paid under a rebate agreement from the determination of best price and average manufacturer price under the Medicaid program.