Portland also traded away guard Sebastian Telfair and center Theo Ratliff to Boston for the No. 7 pick, Randy Foye, then swapped him to Minnesota for the No. 6 pick, Brandon Roy.
Aldridge, a 6-foot-11 power forward/center who played as a sophomore last season at Texas, is known for his defense and could provide immediate help if the Blazers fail to re-sign free agent center Joel Przybilla. He averaged 12.4 points last season and was selected the Big 12 defensive player of the year.
"I really didn't know where I was going to end up," Aldridge said.
Khryapa, a 6-foot-9 Russian forward taken in the first round two years ago, averaged 5.8 points and 4.4 rebounds last season and showed promise when injuries gave him extra minutes.
Making the No. 4 pick before the trade was formally announced, the Blazers took forward Thomas, who played for Louisiana State as a redshirt freshman last season and averaged 12.3 points.
Despite wearing a Blazers hat, Thomas told ESPN he was "looking forward to being in Chicago."
Blazers president Steve Patterson, also serving as interim general manager, said the Blazers wanted Aldridge or Italian forward Andrea Bargnani, who went with the first overall selection to Toronto.
"We had to get up to No. 2 to do it, and we did," Patterson said.
The Trail Blazers dealt Telfair and Ratliff and a 2008 pick to Boston in exchange for the No. 7 pick, center Raef LaFrentz and Dan Dickau. The Celtics took 6-foot-4 Foye out of Villanova.
Foye was an AP All-America first-team selection as a senior last season when he averaged 20.5 points. But his time as a Trail Blazer was short-lived. Soon thereafter, Portland announced the deal with Minnesota for Roy, the Pacific-10 Conference player of the year after averaging 20.2 points for Washington.
"We have a young group," Roy said about the dynamic in Portland. "And now we get to go it together."
The Blazers finished last season 21-61, the worst record in the NBA. And the team's ownership situation is in limbo, with owner Paul Allen claiming the franchise is losing too much money.
Allen, nonetheless, participated in the draft, ensconced at the team's practice facility just south of Portland.
Portland also acquired the 27th pick, guard Sergio Rodriguez from Spain, from the Phoenix Suns for cash considerations. With the 30th overall pick, Portland took Joel Freeland, a 6-foot-10 forward from England.