Hannan, who won the accolade for his Telegraph.co.uk blog, shared the prize with Shikha Dalmia of the US Reason Foundation for work on Forbes.com.
The outspoken MEP was one of three entrants shortlisted for the award, based on 10 submissions of online work.
Earlier this year the Conservative politician criticised the NHS on US television. He later came under fire for listing former Conservative minister Enoch Powell, who held strong views on immigration, as a major political influence in an interview in the US.
As the awards shortlist was announced in August, Marc Sidwell, Bastiat Prize administrator for organisers the International Policy Network (IPN), told Journalism.co.uk that finalists for the prize are 'judged for quality of writing' rather than their public profile.
The award, which was given out at a ceremony on Monday night, is the first time online journalism has been recognised as part of the Bastiat's annual awards, organised by IPN.
John Hasnas, a professor at Washington's Georgetown University, won the $10,000 main prize for his piece on the role of US supreme court judges published in the Wall Street Journal.
The Ecomomist's Robert Guest and Arizona Republic columnist Robert Robb took second and third place prizes respectively in the main category.
Full details of the awards nominees and winners can be seen at this link.