The match has surpassed the previous record of 4 hours, 44 minutes when the score was tied 9-9 in the deciding set.
It was also the second longest match at a Slam, beating the six hours and 33 minutes which Fabrice Santoro spent seeing off Arnaud Clement in the 2004 French Open.
"I don't really know what to say right now", said Anderson. "For us to be out there for that amount of time, I really hope we can address this", he said.
Anderson, who graduated from the University of IL, came through another marathon match to beat Roger Federer in the quarterfinals on Wednesday, winning their fifth set 13-11.
Isner has been playing the tennis of his life this year, claiming a first Masters title and now on the threshold of a first Slam final, and he edgedMilos Raonic, whose body looked to be letting him down once more in a career ravaged with injury.
Anderson finished with 49 aces and 118 winners; Isner had 53 aces and 129 winners.
An Isner ace fittingly concluded the 12 games in the first, before Anderson recovered from a mini-break down to take a one-set lead after an hour and three minutes.
That's how the U.S. Open settles things at 6-all in the fifth set of a men's singles match - or at 6-all in the third set for women - and has since 1970. Between that and the energy-sapper against Isner, it's hard to imagine how the No. 8 seed Anderson will have much left for Sunday's final, his second at a major.
The 12th-seeded Peschke and Melichar came from a break down in the final set to see off the sixth-seeded pairing of Dabrowski of Canada and Xu of China.
How do you sum up Kevin Anderson and John Isner's Wimbledon semi-final? The American roared and turned to his box as he took the third set on his third set point. Another set point came at 9-8, but this time on Isner's serve, who saved it with a 138 miles-per-hour serve.
But not only did Anderson jump back to his feet, the South African astonishingly switched his racket into his left hand and, gripping it half way up the handle, hit a forehand to get the ball back and take the point before he broke and then went on to win the match.
"I feel pretty awful", Isner said afterward.