Satawu's Senzo Mahlangu said a one year agreement was signed, binding to all unions.
"Buses are out there moving. Hours, definition of night shift allowance and other allowances have been increased by 10 percent. Other issues on basic conditions such as relief drivers would be engaged on at next meeting, such issues would be ironed out then," Mahlangu told reporters in Johannesburg.
Labour Minister Mildred Oliphant said the national agreement superceded any agreement signed at company level. She said some employers had pushed for an agreement to be signed separately at provincial level, and that she had advised the negotiators to be guided by the constitution of the bargaining council.
"I was told that Numsa shop stewards had signed for 8.5 percent but their secretary in the meeting this morning said such agreement had been withdrawn. So since the national agreement has been signed by majority of the unions, it will override any agreement at lower level by shopstewards," she said.
Although negotiations would be held at central bargaining level, there would be issues that were relevant for discussions at provincial level, she added. The industrial action, which affected commuter bus services, especially long distance services, began on Wednesday.
There were long queues at bus stations as commuters, in possession of paid bus tickets, were left stranded. The National Union of Metalworkers of South Africa (Numsa) and the Transport and Services Workers Union (Taswu) have rejected the 9 percent wage deal.