1857, "to forgive or pardon" (something wrong), especially by implication, from Latin condonare "to give up, remit, permit," from assimilated form of com-, here perhaps an intensive prefix (see con-), + donare "give as a gift," from donum "gift" (from PIE root *do- "to give").
It is attested from 1620s, but only as a dictionary word. In real-world use originally a legal term in the Matrimonial Causes Act, which made divorce a civil matter in Britain (see condonation). General sense of "tolerate, sanction" is by 1962. Related: Condoned; condoning.