AlphaGo secured the victory after winning the second game in a three-part match with Chinese Go player Ke Jie that took place in Shanghai. The system had won the first of the three planned games on Tuesday.
DeepMind founder Demis Hassabis said that Jie had played "perfectly" and "pushed AlphaGo right to the limit".
In Go, players take turns placing stones on a 19-by-19 grid, competing to take control of the most territory.
AlphaGo has built up its expertise by studying older matches and playing thousands of games against itself, 'BBC News' reported.
The eventual plan is to deploy artificial intelligence in areas of medicine and science, the company said.
Last year the system had defeated South Korean Go grandmaster Lee Se-Dol, winning a sweeping 4-1 series victory.
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