The Phoenix playmaker will go under the knife later this week leaving Ernie Merrick with a big hole to fill during the busy New Year period.
The Costa Rican international suffered the injury after an innocuous challenge in Wellington's 1-0 win over Melbourne Heart on Friday and will go under the knife later this week.
Hernandez, who has shown signs of returning to the kind of form that made him one of the competition's most feared players during his time at Melbourne Victory, was bitterly disappointed upon hearing the news.
"I wanted to play but the physio said it was too dangerous," Hernandez said.
"If I did any more damage to it I could be out for a lot longer.
"It is really disappointing because we have had two wins and the team has been playing very well.
"I was enjoying my football and now I have to miss games."
The 31-year-old, who represented his country during the 2006 World Cup, may now find it difficult to make Costa Rica’s squad for Brazil with Los Ticos scheduled to play two friendlies against Chile and Korea at the end of January, games Hernandez is likely to miss.
Wellington coach Ernie Merrick confirmed the playmaker's injury, insisting that while it isn't ideal his squad is more than capable of covering for their key man as they prepare to take on the Western Sydney Wanderers on New Year’s Day.
"Carlos fell on his wrist and twisted it at the same time. He told us it was aching that night so we had it strapped," Merrick said.
"It seemed fine, but after training the next day the ache was back so we sent him for an X-ray. That revealed a fractured scaphoid bone that needed operating on as soon as possible. He can't play or train till that is done.
"I'll make a decision about who will do that job on match day (but) make no mistake we are going for a win; nothing less."
In more positive news for the club striker Stein Huysegems, who has been struggling with a hamstring strain, pulled up well after the squad’s final training session ahead of the Wanderers clash and is likely to start.