Federal authorities were holding Peter L. Bradley Jr., 40, of Blue Springs, Mo., at Mills-Peninsula Hospital, where he was being treated for bruises and facial scrapes Friday. The co-pilot was taken to the same hospital, where he received eight stitches for a cut to his hand.
There was no immediate word on what charges Bradley faced, Sgt. Joe Reilly said. The FBI and the Federal Aviation Administration were investigating.
Police had no motive for the attack on the flight from Puerto Vallarta to San Francisco on Thursday evening. The plane was carrying 43 passengers and five crew members.
The flight crew fought with Bradley, but had to call for help from first-class passengers. One man told CBS News Early Show Anchor Jon Frankel he was horrified at what he saw.
"I was observing a passenger that I thought had flight sickness, but he ended up taking his shirt off and started harassing the stewardess," the passenger said. "Eventually, he tried to charge the exit. After he hit the door to get in, he opened up the cockpit and attacked one of the pilots."
Reilly said Bradley might have been on drugs or alcohol, or in need of psychiatric medication.
"What really scared me was when he tried to open up an exit," said Chris Honochick, 37, of Salem, Ore., who helped tackle Bradley.
Bradley repeatedly switched seats, disobeying orders to stay put.
He eventually sat in first class, where, Reilly said, he made this threat: "I'm going to kill all of you; keep away from me," while simulating the shape of a gun with his hand.
Bradley allegedly shoved a flight attendant and broke through a locked cockpit door about 7:10 p.m., as the plane flew near Monterey, 115 miles south of San Francisco.
He "was going for the throttle and fuel controls," said Reilly.
During the scuffle, the co-pilot grappled with the assailant, using a tool similar to a shovel or pick to defend himself. The captain used the intercom to ask first-class passengers for help.
Crew members and five to seven passengers wrestled Bradley - more than 6 feet tall and weighing about 250 pounds - to the floor. He was bound with plastic restraints until arrival in San Francisco at 7:50 p.m.
After a delay to gather evidence, the flight continued to Portland, arriving two hours late.