"I want to express my total condemnation of this kind of behavior, which is totally unacceptable in the world of sports, as well as in life," Alonso, a Spaniard, said after practice on Friday.
The Web site asks visitors to place virtual pins, nails and porcupines on a computer version of the Interlagos track to try to keep F1's first black driver from finishing Sunday's decisive race.
Visitors are also invited to "leave a message to Hamilton," and many of them are full of racism and obscenities.
The Web site says, in Spanish, that "Hamilton cannot finish the race" and that "We want Hamilton to lose."
A spokesperson for FIA, Formula One's governing body, denounced the site.
"Discrimination and prejudice can have no place in sports or society," said the spokesperson, who spoke on condition of anonymity because of FIA rules. "Everyone in our sport will join us in condemning these abusive and hateful comments."
Hamilton's boss at McLaren, Ron Dennis, said that if the Web site and its content were "designed to distract the team or Lewis, it certainly is not going to do so."
"We must rise above it," Dennis said. "We refuse to be drawn into something which is widespread through his world in different ways."
Renault boss Flavio Briatore said, "It is completely disgraceful."
Ferrari principal Stefano Domenicali said: "It's not a problem for Lewis, it's a problem for the world."
FIA this year launched an anti-racism campaign after Spanish fans taunted Hamilton during testing in Spain in February. Hamilton last year was at odds with Alonso when the pair raced for McLaren.
Hamilton enters the final race of the year with a chance to win his first title and become F1's youngest champion at age 23. He has a seven-point advantage over Ferrari's Brazilian driver Felipe Massa, and can win the championship by finishing fifth or better Sunday.