Henry clawed the ball back with his hand and crossed for William Gallas to head France's equaliser, a goal that has sparked fierce debate about cheating in football and the need to introduce video technology such as that already used in tennis.
"You can't blame him for carrying on," the 28-year-old Swiss told reporters on Friday as he prepared for the ATP Tour World Finals starting in London on Sunday.
"If the referee doesn't see it, I just think it is the system which is at fault. So many goals are given that weren't goals, this is just one more. I am surprised that this type of error can occur in football."
Federer, who has appeared in television commercials with Barcelona striker Henry, has not always been a fan of the Hawkeye replays that have become a popular feature of tennis.
But he said it was about time that football followed suit.
"I think it needs it more than tennis," he said. "You can't stop play and analyse everything but you can do a few things so things like this don't happen and then Thierry Henry would not be in the position he is in."
World number three Noval Djokovic from Serbia, another keen football fan, said football had to act in the wake of the Henry incident.
"Football needs to have technology, especially after what happened a couple of nights ago.
"I don't want to blame anybody. Of course it was unfair to Ireland but the governing body needs to do something about it.
"At least now, with Hawkeye, we can walk off the court knowing we have won or lost and it was not because of a mistake by an umpire or line judge."
