It comes after a request by the public prosecutor’s office, which is loyal to President Nicolas Maduro.
Mr Maduro was declared the winner of July’s election by the country’s electoral council – most of whose members are also supportive of the president.
But the government has yet to publish any evidence to support its claim of victory, while the opposition says their polling data shows Mr González won easily.
No sooner was the petition received from Venezuela’s public prosecutor’s office than Judge Edward Briceño, who rules on terrorism-related crimes in Venezuela, granted the request and the arrest warrant against Mr González was issued.
“No-one in this country is above the laws, above the institutions,” President Maduro said in quotes cited by AFP news agency in his weekly television program on Monday.
The step represents a significant ramping up of the political tensions in the South American nation.
Mr González was the candidate who ran against Mr Maduro in the country’s recent presidential election. Since the vote, his opposition alliance has published voting data online which it says shows he won the election by a huge margin, of more than 30%.
It is this data that has led to the issuance of the arrest warrant.
He is accused of “serious crimes” including the “usurpation” of public duties, document falsification, instigation of disobedience and system sabotage, according to the public prosecutor.
Mr González, who has been in hiding since shortly after the election, has denied any wrongdoing.
The European Union has refused to recognise Maduro as having won re-election in July without seeing voting results.
Several Latin American countries have also withheld their support, with Mr Maduro’s former ally, President Lula of Brazil, among those calling for full transparency by the Venezuelan government.
The US has recognised Mr González as the winner, saying there is “overwhelming” evidence of Maduro’s defeat.
However, the National Electoral Council declared President Maduro the winner, prompting major protests across Venezuela.
The government of President Maduro has detained more than 2,400 people since the election, creating what the UN has called “a climate of fear”.
Now, the possibility that Mr González may also be detained on charges of inciting public disorder and conspiracy has suddenly become far more likely.
Earlier, the US Department of Justice seized a plane used by President Maduro, saying it was obtained in violation of US sanctions on Venezuela.
In response, President Maduro’s government accused Washington of “piracy” and of “illegally imposing its will” around the world.
