The 26-year-old accelerated away from race favourite and compatriot Jonathan Kosgei Kipkorir in the closing kilometres to clock two hours 12 minutes and 40 seconds, inside the previous ACM best of 2:12:42 by Paul Lekuraa in 2008. Edwin Kimutai was third.
The course record is two hours 10 minutes 55 seconds set by Italian Stefano Baldini at the 2004 Olympics.
"This is an amazing feeling for me because it is the first time I have won a marathon," said Bett Kimutai after finishing inside the Panathenaic marble stadium, home of the first modern Olympics in 1896.
"The course is very different to other marathons, with some difficult hills and lots of climbing. It is very tough but it is a great course and a different feeling to run here."
The first woman to cross the line was 29-year-old Lithuanian Rasa Drazdauskaite who also set an ACM record of 2:31:06, beating Russian Svetlana Ponomarenko's 2007 mark of 2:33:19.
The ACM has taken on special significance this year as it is the 2,500th anniversary of the fabled 490 BC run of Athenian messenger Pheidippidis who is said to have run from Marathon to Athens to announce victory over the invading Persian army.
A record 12,500 runners, more than three times the usual amount, took part on Sunday including a record 3,000 Greeks.
The total number of participants, including the 10-km and 5-km races, swelled to 20,500.
Greek Prime Minister George Papandreou was among the runners in the 10-km race.
"Today is a celebration for all of humanity," said Papandreou.
"Greece is running a marathon of its own at the moment and we also hope to finish soon," he added, referring to the country's economic strife.
ACM organisers said they expected to the Greek capital to benefit by an estimated 25 million euros as a result of increased tourism during the celebrations.
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