Along with Tiger Woods and Henry, Fed Express forms sport's holy trinity promoting shaving giant Gillette in a multi-million dollar contract.
Gillette have announced they are to stand by Henry, despite his cheat shame which robbed the Republic of Ireland in Paris on Wednesday night, and Federer said the fault lay with football's refusal to embrace new technology.
He said: "I don't condone what happened, and I don't think it's appropriate, but it happened in a split-second and ultimately it was the referee's decision. You can't blame him (Henry) for playing on - it's the fault of the system."
Federer, who hates the Hawkeye gadget which settles contentious line calls in tennis, added: "It goes to show football needs Hawkeye more than tennis."