The court ruled on Monday that more than 800,000 pro-vote signatures questioned by electoral authorities should be considered valid.
Opposition leaders welcomed the ruling as opening the way for a recall vote this year on Chavez's rule.
But the government, which has rejected the referendum attempt as riddled with fraud, immediately appealed to a higher level of the court against what it called a flawed decision.
Opposition supporters in east Caracas celebrated the court ruling by honking car horns, blowing whistles and waving national flags.
The court ordered the National Electoral Council to lift its objections to 876,017 pro-referendum signatures originally questioned because their petition forms contained examples of similar handwriting.
"This looks like a step in the right direction for the opposition, but the government will probably do everything in its power to undo the decision"
VenEconomy consulting firm
It said those signatures should be added to more than 1.8 million already declared valid by the council and not be subjected to individual confirmation checks as previously planned.
That gave the opposition a potential total of 2.7 million valid signatures, above the the minimum 2.4 million legally required to trigger a referendum, although further checks and a final decision by the council were still pending.
"The Electoral Chamber has put an end to the tricks, assaults and ambushes that the government was playing through the National Electoral Council," said Henry Ramos of the Democratic Coordinator opposition coalition.
Opposition leaders had appealed to the Supreme Court after accusing electoral council officials of favouring Chavez by unfairly objecting to tens of thousands of signatures.
Pro-Chavez National Assembly deputy Ismael Garcia said the government was asking the Supreme Court's Constitutional Chamber to overturn the Electoral Chamber ruling.
"This is an unprecedented judicial assault and aberration, it's a new trick by the opposition that will soon be dismantled," he said.
The opposing views signaled a fierce jurisdictional battle within the Supreme Court, which like many state institutions in Venezuela is split between political followers and foes of the president, who was elected in 1998.
"This looks like a step in the right direction for the opposition, but the government will probably do everything in its power to undo the decision," said Robert Bottome of the Caracas-based VenEconomy consulting firm.
Nine people were killed in street
clashes in Caracas last month
The referendum dispute in the world's Number 5 oil exporter turned violent late last month.
At least nine people were shot dead and dozens injured in several days of street clashes between troops and pro-vote protesters in Caracas and other cities.
Opponents of Chavez, whose term ends in early 2007, say his self-styled "revolution" threatens to turn oil-rich Venezuela into another communist Cuba.
He accuses his enemies of trying to overthrow him with US help, something Washington denies.