The traffic on the M1 highway from Soweto towards the Crown Interchange was at a stand still, the Johannesburg metro police said on Tuesday.
JMPD spokeswoman Edna Mamonyane said traffic was "chock a block" and that it had not eased up since the early morning.
That route is not tolled and is close to the N1 which is subject to e-tolls.
Tuesday marked the first day of the controversial e-tolls, managed by Sanral, which compels motorists to pay to use certain highways around Gauteng via an e-tag.
Mamonyane said: "Coming in from the west; Hendrik Potgieter, Ontdekkers and Main Reef roads are heavy, which happens on a daily basis."
Kliprivier, Booysens and Rosettenville roads were backed up for motorists coming from the south of Johannesburg, she said.
"Normally in the north, [roads such as] William Nicol and Beyers Naude are very heavy."
She said motorists were using suburbs as alternative routes.
"People are going to start seeing a heavy presence of cars in their [neighbourhoods]. A lot of it will be from the northern suburbs," she said.
Mamonyane could not immediately confirm which other alternative routes were being used by motorists.
At least two anti-e-tolling media briefings are planned for Tuesday.
One will be by the Congress of SA Trade Unions in Gauteng, which has been protesting against the project to "irritate politicians", and one by the opposition Democratic Alliance which would unveil the "next phase" of its anti-tolls campaign.
Church leaders vowed on Monday that they would not pay toll fees, and called on others to do the same.
The Opposition to Urban Tolling Alliance (Outa) continued to urge motorists to refrain from buying e-tags.
"There is no law that requires road users to buy an e-tag or register with Sanral in order to use Gauteng's freeways," said Outa chairman Wayne Duvenage. -Sapa