"The constituent assembly lacks legitimacy and because of that we cannot accept the result," he said.
Venezuela's President Nicolás Maduro called the vote as protests against his government gained momentum in May.
The opposition sees it as a move towards dictatorship.
The new constituent assembly, comprising 545 members, will rival the National Assembly, currently controlled by the opposition.
"We insist on a peaceful solution for the country's situation," said President Santos.
Earlier on Friday, police in the Venezuelan capital Caracas fired tear gas and rubber bullets against opposition activists who blocked roads. At least two people were injured.
Venezuela has banned protests that could "disturb or affect" the vote.
Prison terms of between five and 10 years could be imposed on those contravening the ban, Interior Minister Néstor Reverol said on Thursday.
The ban on activity will remain in force until Tuesday.
The situation has worsened to the point that the United States has ordered family members living at the embassy in Caracas to evacuate the country. It also authorised its staff members to leave if they desire.
Mr Maduro said his opponents should "abandon the road to insurrection" and added that he would be willing to begin a "roundtable dialogue in the next few hours".
On Wednesday, the US imposed sanctions on 13 senior Venezuelan officials, including Mr Reverol.
The sanctions freeze the US assets of those targeted and stop American entities from doing business with them.
President Donald Trump promised "strong and swift economic actions" if the poll goes ahead.
Mr Maduro responded by describing the US as imperialists bent on ruling the world and called the sanctions "illegal, insolent and unprecedented".
More than 100 people have been killed in protest-related violence since April.