"There has been a misunderstanding on the side of management, who said the workers were on strike … they held a meeting with the union and later sang slogans outside the building," South African Municipal Workers' Union spokesperson Tahir Sema said on Monday.
Most of the employees would return to their workplaces, he said.
"We will attempt to resolve these issues with management as soon as possible. If management agrees, we will be meeting them in the coming weeks to finalise workers' legitimate workplace concerns."
Pikitup said earlier on Monday that only a fraction of their workers turned up for work in the morning.
Most of them were demonstrating outside the company's headquarters, spokesperson Desiree Ntshingila said.
At the weekend the company obtained a court interdict to stop the strike, which it considered illegal.
Ntshingila said they would meet with unions later on Monday.
Workers' grievances included the implementation of biometric access control, breathalyser tests for drivers and transport for workers.
On Sunday, Pikitup said the current transport system for workers was not sustainable and a new solution was needed.
"Previously, Pikitup employees requiring transportation were picked up and dropped off at central points on a daily basis, using Pikitup trucks," managing director Amanda Nair said in a statement on Sunday. "It is unfortunate that our employees have resorted to an unprotected strike in relation to their grievances."
"We will not tolerate such disregard for the law and will take swift legal action in dealing with all involved," she added.
Sema said workers were not happy with Pikitup's biometric clock-in system and the apparent lack of consultation about its implementation.
"Workers want the employer to provide travel arrangements, and they are not happy that the management took away the half-day off they were given once a month, as a result of overtime work." – Sapa