The awards ceremony took place on Friday evening in the Kadriorg Art Museum in Tallinn.
Tallinn had already hosted the 2013 European Athletics Awards Night in October.
Kanter was rewarded for winning bronze this year at the IAAF World Championships in Moscow. In fact he has not left the podium in the World Championships since 2003 and earned gold at Osaka 2007.
He is arguably the best Estonian athlete over the past decade, winning the Olympic title in Beijing in 2008.
Continuing an Estonian tradition of honouring Olympic gold medallists with a postage stamp, a Gerd Kanter stamp was issued on September 2008.
However Kanter is still missing a European Athletics Championships gold medal which he hopes to add to his collection at the Letzigrund stadium in Zurich next summer.
Anna Iljustsenko won the women’s athlete of the year prize. She cleared a new indoor high jump national record with 1.94m.
She also placed third at the Universiade Games and was fourth at European Athletics Indoor Championships in Gothenburg
Both their coaches Indrek Tustit and Gaspar Epro were named Estonian coaches of the year.