The announcement came on the Chelsea striker's 32nd birthday and it is his second award, after he also won in 2006.
Drogba helped his country through a convincing World Cup qualifying campaign in 2009, during which he scored five goals as the Ivorians finished unbeaten.
But while he scored in the FA Cup final his achievements at club level were not as significant as those of 29-year-old Eto'o, who will have legitimate reason to feel he should have won a record fourth award.
The award was decided by a vote of Africa's national team coaches although the final tally was not immediately made available by the Confederation of African Football (CAF).
Eto'o, who also had a birthday this week, scored for Barcelona in May's UEFA Champions League final and also won league honours in Spain before moving to Inter Milan.
Eto'o was also pivotal in Cameroon turning around their World Cup qualifying campaign after new coach Paul Le Guen appointed him captain in August.
Cameroon came from bottom of their group to top the standings and qualify for this year's finals in South Africa.
Drogba had narrowly edged out Eto'o for the 2006 award by just 79 votes to 74.
The Cameroon captain was African Footballer of the Year in 2003, 2004 and 2005, when he beat Drogba by only two votes.
Drogba's Chelsea team mate Essien, who was among the final three candidates for a fifth successive year, has never won the award.
The 2008 prize was lifted by Emmanuel Adebayor of Togo but the Manchester City striker did not make the shortlist for the 2009 award.
None of the three candidates travelled to Ghana's capital for the annual awards at which World Cup-bound Algeria were named Team of the Year.
Algeria beat African champions Egypt in a sudden-death playoff to reach this year's World Cup finals.
