Moynihan's success will cause some disquiet in Whitehall after his criticisms of Government sports policy, especially as he will now play a key role in the preparations for the 2012 Olympics in London.
With Moynihan's friend, Lord Coe, already the chairman of London 2012, it means there are now two Tory peers in senior positions connected with a Games which the Government wants to be seen as a New Labour legacy.
Moynihan promised to put political rivalries aside and insisted he has stepped down from politics even though he will retain the Tory whip in the House of Lords. "Government ministers recognise a constructive approach is critical. I believe we have a duty to work effectively and constructively with Government," he said.
The 50-year-old won the majority of the 43 votes - the 28 summer Olympic and seven winter Olympic sports each had a vote as well as individual members of the BOA.
Moynihan will be one of four members of the 2012 Olympic Board along with Coe, the culture secretary, Tessa Jowell, and the London mayor, Ken Livingstone.
Jowell signalled her intent to get off on the right foot by issuing a message of congratulations. "The close co-operation between Government, the mayor and the BOA was a key factor in our success [in winning the 2012 games]," she said.
"We share a common objective: the overriding determination to host a first-class Olympics and to extend the opportunity to excel to a new generation."