Secure Domestic Container Partnership Act of 2004 - Amends Federal shipping law to direct the Secretary of Homeland Security to carry out an empty shipping container sealing pilot program to encourage shipping container handlers to seal empty shipping containers after they have unpacked them. Allows the Secretary to authorize a shipper, cargo carrier, freight forwarder, terminal operator, port authority, or labor organization that is a qualified container handler to secure, under a seal approved by the Secretary, a shipping container that is emptied by the person.