He was immediately replaced by new president and chief executive Harry Stonecipher, 67, and by new non-executive chairman Lewis Platt, 62, the company said.
"Boeing is advancing on several of the most important programmes in its history and I offered my resignation as a way to put the distractions and controversies of the past year behind us, and to place the focus on our performance," Condit said in a statement.
Boeing sacked chief financial officer Mike Sears recently for improperly recruiting a US Air Force official, Darleen Druyun, at the time she was involved in decisions that affected the company.
Druyun, also fired by Boeing, was closely involved in the $18 billion deal under which the air force would have received 100 new re-fuelling jets from Boeing.
Defence Secretary Donald Rumsfeld has said the Pentagon is investigating whether to suspend the deal.
Stonecipher had retired in May
Earlier this year, the aviation and aerospace giant had been sanctioned by the Pentagon for obtaining secret documents from its chief competitor, Lockheed Martin Corp., for a bid on a rocket project.
The new Boeing boss, Stonecipher, had retired from the company in 2002 after working closely with Condit for five years in several roles including vice chairman, president and chief operating officer.
Stonecipher said Boeing had to rebuild its reputation. "We have the right strategy. The task before us is to execute. We need to strengthen our reputation with our customers, employees, investors and the communities in which we operate," he said.
Platt, the non-executive chairman, has been a member of Boeing's board of directors for four years. He was former chairman, president and chief executive of computer group, Hewlett-Packard.
Platt said Condit had acted with "characteristic dignity and selflessness" in recognising that his resignation was for the good of the company.