He was trailing 5-3 in the next group tie-break when the point was ceased after he heard a shout from the crowd.
Umpire Carlos Bernardes ruled Edmund had lost the point because of this, with the Briton saying:”They keep screaming every stage, I keep hearing it.”
Isner served an ace on the next point to summary a 7-6 (7-5) 7-6 (7-3) win.
Defending champion Isner served 17 pros and won 81 percent of first-serve points as he beat the 19th seed.
Isner hurried to an early lead and needed treatment on his back before serving to get the opening series at 53.
But he was busted to love by Edmund, who won 2 of those final three matches to force a tie-break.
The Briton led the tie-break 52 however some big serves from Isner along with also an Edmund double fault levelled the decider at 5-5, before Isner served outside the group.