The World Series champions sent reliever Mark Melancon and minor league infielder Jimmy Paredes to Houston for the former All-Star first baseman, who will become the Yankees' designated hitter. Houston will pay $4 million as part of the deal.
On Friday, New York obtained outfielder Austin Kearns from Cleveland for a player to be named or cash.
Berkman didn't play Friday night against Milwaukee, and his Astros teammates said their goodbyes.
A five-time All-Star, Berkman had full no-trade rights and his approval was necessary for a trade, accounting for the delay in its completion.
"I'm from Texas. Heck, I played at Rice. This city is like the womb. I feel very comfortable here. To think about the possibility of going anywhere else is kind of scary," Berkman said Friday night.
After the game, Astros rookie Chris Johnson embraced Berkman.
"It's really an odd feeling seeing his locker cleaned out," Johnson said. "He came up and jumped on my back and gave me a hug and said, 'Keep up the good work' and, 'Good luck.' It was weird."
To fill Berkman's roster spot, the Astros selected the contract of first baseman Brett Wallace from Triple-A Round Rock.
The 34-year-old Berkman is hitting .245 with 13 homers and 49 RBIs. He has 60 walks and 70 strikeouts in 298 at-bats.
"I think it would be good for him," said pitcher Roy Oswalt, traded from Houston to Philadelphia earlier in the week. "Sometimes you get a change of scenery — turns you all the way around. Sometimes you get in a rut of doing the same thing over and over again."
Berkman said Astros general manager Ed Wade discussed the possibility of a trade with him.
"He approached me two days ago with a list of probably eight teams that had expressed some interest. There were four yeas and four nays. There were some that were just no possibility," Berkman said.
"In one way, it's good if there are teams that still want me to play for them. That makes me feel pretty good, particular in a down season," Berkman said. "I still have confidence that I could play at a high level. It's a good feeling to hear these trade rumors. Obviously, these scouts from other teams feel that same way or else I wouldn't be in the conversation."
Berkman fills the DH slot originally intended for Nick Johnson, who returned to the Yankees during the offseason. The brittle Johnson has been on the disabled list since May 8 with a right wrist injury that required surgery.
Berkman, last an All-Star in 2008, is making $14.5 million this year. His contract includes a team option for 2011 at $15 million with a $2 million buyout.
Of the slightly more than $7.15 million remaining on the contract, the Yankees will pay $3,150,273.
"You don't always get to pick how you leave an organization," Berkman said. "If and when it comes time to move on, I'll do it with as much grace as I can muster."
Kearns left Cleveland's game on Friday night at Toronto in the seventh inning. The former first-round draft pick is hitting .272 with eight homers and 42 RBIs.
"A corner outfielder that gives us depth and experience," Yankees manager Joe Girardi said. "A right-handed bat that has power. We can use him a lot of different ways. It will give me a chance to rest our left-handed guys."
Kearns was to join the Yankees on Saturday.
"That's great," Yankees first baseman Mark Teixeira said. "Two quality guys. I know both of them real well. They're both great guys. It's going to be good for the clubhouse."
Kearns was looking forward to playing in Yankee Stadium.
"Whether you're on the home or visiting team, it's fun. You've got a packed house and you know you're playing on a winner," he said. "You can't ask for anything more."
AP freelance writers Mark Didtler in Tampa, Fla.; Rich Dubroff in Washington; Ian Harrison in Toronto; and Michael A. Lutz in Houston contributed to this report.