Apparatus and method for applying pre-molded seal caps to fasteners. The apparatus includes an installation tool and a disposable cap holding fixture. The installation tool includes a body and a handle. A plunger can pass through the body and handle. A disposable cap holding fixture can be connected to an end of the body of the installation tool. The disposable cap holding fixture can grip a surface of a pre-molded seal cap. The pre-molded seal cap can then be placed on a fastener and the disposable cap holding fixture can be rotated to rotate the cap to cover the fastener with uncured sealant in the cap. The body and handle can be rotated by an operator or the body can rotate about the handle and actuation of the plunger can cause the body and the cap holding fixture to rotate. The plunger can then dislodge the cap from the fixture.