But its creators had been bullish going into the match at the Four Seasons hotel in the South Korean capital, saying the computer, which employs algorithms that allow it to learn and improve from matchplay experience, was even stronger than when it took on Fan.
"We are very, very excited by this historic moment and very, very pleased with how AlphaGo performed," Demis Hassabis, the CEO of AlphaGo developer DeepMind, said after the victory.
"We think that Lee will come up with new strategies and... try some different things tomorrow. We'll have to see how AlphaGo will deal with it," Hassabis said.
The match-up sparked enough interest to warrant an Internet live-stream as well as live TV broadcasts in South Korea, China and Japan.
"I was shocked. Everyone was," said Kim Seong-Ryong, a Korean Go commentator and professional player.
"Something none of us thought would happen has just happened."
The five-day battle for supremacy between man and machine has been seen as a major test of what scientists and engineers have achieved in the sphere of Artificial Intelligence over the past 10 years or so.