They started simultaneously just after 11:00 on Friday.
In Johannesburg, protesters whistled, danced, and sang Cosatu songs as they marched down Bree Street, taking up about half a block in the city's CBD.
In addition to showing their rejection of plans to toll freeways in Gauteng, Cosatu is also objecting to the recent housing demolitions in the province.
Four memorandums were expected to be delivered in Johannesburg and Pretoria to the housing, finance, and transport departments in both cities.
Cosatu provincial secretary Dumisani Dakile called for a commission of inquiry into the e-tolling project.
"We want to know who are the contractors and sub-contractors... There is a need for a commission of inquiry into the e-tolling system," Dakile told transport department official James Molao before handing over a memorandum to him, the Sapa news agency reported.
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