The truck went into the water shortly after 1:35 p.m. near the 2800 block of Seventh Street.
The truck was apparently knocked into the water by some sort of machinery and the man was underwater for more than 30 minutes before port divers could reach the vehicle and retrieve the body, Oakland fire Battalion Chief Coy Justice said.
The truck has also since been retrieved from the water, Justice said.
The man's name has not yet been released by the Alameda County coroner's bureau, but a co-worker said he was a 79-year-old man who had worked at the port for more than five decades.
"He's a very loved man, he's like a father to all of us," said Frank Gaskin, a business agent with International Longshore and Warehouse Union Local 10.
Gaskin said work will shut down at the port until Saturday in honor of the employee and while authorities investigate the incident.