The 752-foot Overseas Reymar rammed the tower on Monday afternoon as it headed out to sea, according to the Coast Guard and state transportation officials.
The unidentified pilot will also report to the state Board of Pilot Commissioners, which will conduct its own investigation of the accident. That board regulates bar pilots.
The pilot has been a San Francisco bar pilot since 2005, said Charlie Goodyear, a spokesman for the San Francisco Bar Pilots Association. The association did not release his name.
Coast Guard spokesman Shawn Lansing said the pilot and others on board during the accident will be tested for drug and alcohol use "per federal regulations."
Lansing said investigators will inspect the hull above and below the water line and are exploring possible factors. Visibility at the time was about a quarter-mile, but officials didn't say if that was a factor.
"There's always the human factor," Lansing said.
Lansing said the ship's double hull wasn't breached, and state officials said the bridge sustained minor damage but remained opened immediately after the accident. The crash damaged 30 to 40 feet of "fender" material that will need to be replaced.
Monday's mishap brought back memories of a major crash in November 2007 in which the 902-foot Cosco Busan rammed the bridge and spilled 53,000 gallons of oil into San Francisco Bay.
That accident contaminated 26 miles of shoreline, killed more than 2,500 birds and delayed the start of the crab-fishing season. Capt. John Cota, the pilot of the Cosco Busan, was sentenced to 10 months in prison after pleading guilty to two misdemeanors.
The mishap Monday did not affect traffic on the busy bridge - the main artery between San Francisco and Oakland.
The parent company that owns the Marshall Islands-registered ship, OSG Ship Management Inc., said the accident occurred as the vessel hit an underwater portion of the massive bridge structure. The Overseas Reymar was not carrying oil as cargo on Monday, only fuel to power its engines, said Goodyear.
The Coast Guard said no oil or hazardous materials were reported to have leaked into the water. Still, officials spread 4,000 feet of absorbent material on the water to be safe.
No crew members on the ship were injured, and its hull appeared to suffer some scrapes and minor indentations, Goodyear added.
"There's all kinds of speculation as to whether the ship had been pushed into the fender by a strong tide, rather than a head-on collision," Goodyear said. "In comparing this to 2007, this appears to be a much lesser impact."
The crew of the Overseas Reymar reported no loss of steering or propulsion, and initial investigations showed no water leaks from any of the ballast tanks, said Darrell Wilson, a spokesman for OSG.
"The ship's crew safely anchored the vessel and made all proper notifications to the authorities," Wilson said.
California Emergency Management Agency spokesman Jordan Scott said the superstructure of the bridge was fine.
"There is some damage to the vessel, but nothing that poses a danger to anybody," Scott said. "A fire boat is out there to make sure it stays that way, and it should."
The tower of the bridge appeared to be fine from a distance, added California Department of Transportation spokesman Bart Ney. A fender system made of steel and wooden timbers was built onto the west span to absorb such strikes, he said.
Investigators have not yet said why the crash occurred. The tanker docked west of Yerba Buena Island immediately following the crash.
State law requires a bar pilot to guide every large vessel - be it a luxury liner, a billionaire's yacht, aircraft carrier or cargo ship - in, out and around the San Francisco Bay.
The pilots' role came under intense scrutiny in the crash of the Cosco Busan. The companies responsible for the Cosco Busan paid close to $60 million for the cleanup and in criminal fines.