According to the Wall Street Journal, the fire damaged six warehouses belonging to Brazilian sugar giant Copersucar, threatening to put the terminal out of action for at least six months while repairs are made.
In total, some 10 percent of Brazil's total monthly sugar exports were lost to the fire, while a fifth of the nation's future exports may be jeopardised over the coming months.
Reuters reported that traders immediately rushed to cover short positions, sending raw sugar prices up 6 percent to 20.16 cents a pound, while futures closed up 0.50 cents, or 2.5 percent higher, at 19.50 cents per pound.
"The size of Copersucar's export terminal will make it difficult to finish construction in less than a year, so we will not be back to the same export capacity soon," told Tarcilo Rodrigues at analysts Bio Agencia to Reuters.
"It's going to be very complicated to find an alternative (port), especially since other ports are working with contracts that run through the end of the harvest" in April, added Nicolle Monteiro de Castro, an analyst at SA Commodities, a Santos-based brokerage and shipping agency, to WSJ. "We're still not sure how Brazil's sugar will be shipped since there isn't enough capacity at other ports."
Copersucar represents 47 sugar mills in Brazil and recorded revenue of $4.1 billion in 2012. The company had hoped to expand its annual trading volume to 9 million tonnes this year. In 2012, Copersucar had exported 7 million tonnes of sugar of the 24 million that Brazil exported.
Brazil meanwhile is the world's largest sugar producer, accounting for about a fifth of global output. The port Santos exports about 60 percent of Brazil's raw, granulated sugar to buyers in places such as Saudi Arabia and Russia.
Copersucar is still studying the damage and hasn't made estimates on how long it will take to rebuild the warehouses, said Leonardo Aragão, a spokesman for the company.
Experts the WSJ spoke to, say removal of the debris from the blaze and rehabilitation of Copersucar's port complex could take as long as 6-18 months. That means Brazilian shipping capacity may compromised through the end of the next harvest in 2015.
"The sugar itself is the least of their worries," told Phil Pia, a trader at Brazilian mill Grupo Andrade, to WSJ, "They won't be loading any sugar out of that terminal anytime soon. The loss of Copersucar is going to tighten up logistics considerably."
US-based Price Futures Group senior analyst Jack Scoville was more optimistic.
"The loss of the warehouse space in ports will make shipping much more difficult. So we saw a short-term spike in prices, but as the logistical issues get worked out, we will see this go away," he told AFP.
"It will hurt world availability for the short term, though, and probably help India and Thailand sell sugar at slightly better prices than they might have been able to do otherwise."