Lee Sedol, one of the best Go players in the world with 18 world championships, was grim and ashen after the game, which lasted more than four hours.
"I'm quite speechless," he said at the press conference that was livestreamed on YouTube. "It was a clear loss on my part. From the beginning there was no moment I thought I was leading."
The latest victory by AlphaGo over South Korea's Lee puts Google's AlphaGo team one victory away from claiming the $1 million prize.
If AlphaGo wins, the prize money is to be donated to UNICEF, Go organizations and charities.
AlphaGo's first win against Lee, on Wednesday, shook the Go-playing world, marking a milestone in the development of artificial intelligence.
Hundreds of thousands of South Koreans, even those who do not play the popular board game, followed the games on live TV and on YouTube. All major local newspapers reported Lee's loss on their front pages.
"2-year-old artificial intelligence masters 5,000-year-old human Go," said a headline in the Chosun Ilbo, South Korea's most circulated daily newspaper.
Many had believed it would take another decade for computers to conquer the ancient Chinese board game, one of the most creative games ever devised and the only board game left to conquer after chess was mastered by computers in 1997. Go is much more complex than chess.
Google's team compared AlphaGo's win to landing on the moon.
The three remaining games run until Tuesday. Even if Lee loses the third game, he will play all five games.
Lee, 33, brimmed with confidence two weeks ago but that confidence was missing after two straight defeats.
"The third game is not going to be easy for me," he said.
The world champion of the ancient board game Go, South Korean Lee Sedol, expects to prevail in a match with Google's computer program AlphaGo next month, but he's not so sure he will be able to do so a year later.
Computers eventually will defeat human players of Go, but the beauty of the ancient Chinese game of strategy that has fascinated people for thousands of years will remain, the Go world champion said Tuesday.
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