But reports showed shops and businesses were open in Harare, Zimbabwe's capital, and witnesses said the strike had failed to take off in other major centres around the country.
With almost a quarter of people in jobs earning less than a dollar a day, many cannot afford to stay away.
"Things are hard enough already and I cannot afford to stay at home and gamble with my job or my security," said a worker at a textile company.
One woman told Al Jazeera: "If you can consider our salaries, they are very low. But what you do when you are at work is what counts. Maybe you can use the phones ... that's why you have to go to work - for that phone call, which is free."
The union's planned two-day work boycott had been intended to increase pressure on Robert Mugabe, Zimbabwe's president, as his government grapples with inflation, officially put at 6,592.8 per cent.
"We want jobs and food on the table for the people of this country and we hope this is the key to resolving the national crisis"
Wellington Chibebe, the ZCTU secretary general, described the response to the boycott as "mixed".
"We are touring the industrial areas right now and we have noticed that some factories are opened, but what we have also noticed is that some workers did not turn up for work," he said.
Al Jazeera's Haru Mutasa, reporting from Harare, said that while the strike seemed to be having little effect, talk in the capital was focusing on the deal reached by Mugabe's government and the two factions of the opposition Movement for Democratic Change (MDC) a day earlier.
In a compromise deal on Tuesday, both factions of the MDC agreed to a constitutional amendment that allows parliament to elect a new president if the incumbent does not serve a full term.
This move would effectively allow Mugabe to choose his successor, provided that he stood down.
Nelson Chamisa, spokesman for the faction of the MDC led by Morgan Tsvangirai, denied that the opposition had caved in.
Instead, he said the agreement was a result of negotiations with Mugabe's Zanu-PF party.
"We want jobs and food on the table for the people of this country and we hope this is the key to resolving the national crisis," he said.
Critics say Mugabe's economic policies, which include ordering businesses to stop raising prices and salaries to try to tame inflation, have brought Zimbabwe to its knees.
Mugabe denies the allegations and accuses Western powers, which have imposed targeted sanctions on Zimbabwe, of sabotaging the country's economy and plotting with the opposition to oust him.