No, a section 501(c)(3) organization may not make a contribution to a ballot measure committee. According to IRS Publication 1828, section 501(c)(3) organizations are explicitly prohibited from making contributions to ballot measure committees. This prohibition is part of the broader restrictions on political campaign activities that apply to these organizations to maintain their tax-exempt status. Violation of this prohibition can result in the denial or revocation of tax-exempt status and the imposition of excise taxes.
Sources:
Rev. Rul. 81-95
Rev. Rul. 2007-41
Publication 1828 (8/2015)
Rev. Rul. 2004-6
PLR 200151060
