The match against Isner was the second-longest in professional tennis history, behind only Isner's record-setting 11-hour, five-minute first-round Wimbledon triumph over Frenchman Nicolas Mahut in 2010.
"I don't really know what to say right now," said Anderson.
"Just playing like that in those conditions, it was really tough for both of us.
"John's such a great guy and I really feel for him because if I'd been on the opposite side, I don't know if I could take that, playing for so long and coming up short.
"You feel like this is a draw for the two of us, but somebody has to win.
"So I apologise if I'm not more excited right now because the mix of emotions getting through something like that is quite different."
The last set alone lasted five minutes shy of three hours and Anderson said it was unfair on both players.
"I really hope we can look at this and address this because in the end you don't even feel that great out there," the eighth seed said.
The US Open is the only grand slam to use tiebreakers in the fifth set, with the Australian Open and French Open, like Wimbledon, both also playing advantage sets.
Twitter was abuzz with jokes that the Anderson-Isner match could well stretch beyond the 70-68 final-set scoreline that Isner won with over Mahut eight years ago.
That "endless match" prompted officials to erect a plaque on Court 18 to commemorate the feats of the two players.
Many would argue Anderson and Isner deserve similar recognition after the great mates warmly embraced at the net before receiving a standing ovation from tennis's most famous centre-court crowd.
Anderson's prize for his bittersweet victory over his former US college friend and rival is a date on Sunday with either world No.1 Rafael Nadal or fellow grand slam giant Novak Djokovic.
The ridiculous length of the Anderson-Isner clash left Nadal and Djokovic waiting until 8pm (local time) before stepping on court for their box office semi-final.
The roof was closed and Nadal and Djokovic had until the 11pm club curfew to finish or return on Saturday, the traditional rest day for the two men's semi-finalists.
Should Nadal prevail in the duo's record 52nd showdown, the Spaniard will play Anderson in a repeat of last year's US Open final in New York.