After beating eight-time champion Roger Federer, also over five sets in the quarter-finals, 2017 US Open runner-up Anderson claimed his 300th career win.
The match has surpassed the previous record of 4 hours, 44 minutes when the score was tied 9-9 in the deciding set.
"I really hope this a sign for grand slams to change this format. Somebody has to win, John is such a great guy and I really feel for him", added Anderson, who has known Isner for 14 years.
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But no one expected the longest match played on Centre Court in history, one with a load of nerves. Isner and Anderson have played each other before professionally and they were rivals in college (Isner, 33, played at the University of Georgia, and Anderson, 32, at University of Illinois).
Novak Djokovic was leading Rafael Nadal 6-4, 3-6, 7-6 (9) in a compelling showdown filled with entertaining points that was suspended as soon as the third set concluded at just past 11 p.m., the curfew at the All England Club.
Isner is still seeking his first Grand Slam final appearance. In most cases, this is still a compelling finish, but when you put two heavy-hitting goliaths against each other, what results is a six-hour slog that can cause delays across the tournament.
The eighth seed will face either twice champion Rafael Nadal or three-times victor Novak Djokovic in Sunday's final.
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In a matchup of two of the tallest (Isner at 6 feet, 10 inches, Anderson at 6-8) and biggest-serving players on the ATP tour, Isner and Anderson expectedly played tiebreaks in each of the first three sets.
After Anderson dropped the second set on a tiebreak despite making only one unforced error, a see-saw third set full of momentum changes followed, with both men creating chances, but unable to take them. The record, funnily enough, was set by Isner.
One of Anderson's best plays came in that lengthy final set. He made it 0-30 in that game by winning a point after falling on his back behind the baseline but still got up in time to return Isner's shot.
The world was a demonstrably different place when Kevin Anderson and John Isner first took the court Friday for what would become a marathon Wimbledon semifinal. "I felt like I did some good business here in the past already", he said.
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"I don't really know what to say right now".