More than 40 African countries signed a free trade pact on Wednesday that the nations hope will fulfill a long-held dream of greater economic integration on the continent.

But among the holdouts are two of Africa’s biggest economies, Nigeria and South Africa, raising concerns about whether the agreement can make good on its promises.

The African Continental Free Trade Area, which has been in the works for two years, aims to unite participating countires into a single trading market that would be one of the largest free trade zones in the world since the World Trade Organization was created in 1995.

Of Africa’s 55 countries, 44 signed the pact.

“Amongst African states in general, there has long been a hankering for a trade agreement that transcends national boundaries,” said John Campbell, a senior fellow and Africa expert at the Council on Foreign Relations in New York. “In Africa more than any other part of the world, national boundaries are seen as artificial, essentially as a colonial imposition.”

“Moving from an aspiration to the actual specific words on a page, of course, becomes very much more complicated,” he added.

Of the 11 holdouts, Nigeria and South Africa represent $700 billion — or one-third — of the $2.1 trillion in gross domestic product across all 55 African countries.

The two countries are also home to 242 million people, or 20 percent of Africa’s population of 1.2 billion.

“It will have a huge effect on the agreement if they remain on the outside,” said Joshua Meservey, a senior policy analyst on Africa and the Middle East at the Heritage Foundation. “I wouldn’t say it would cripple the agreement, but it will badly damage it.”

Nigeria, the continent’s largest economy, was the most notable drop-out.

Muhammadu Buhari, the president of Nigeria, abruptly canceled his trip to Kigali, Rwanda, where the agreement was signed. Though his cabinet had said the agreement would create jobs and foster growth, officials said more time was needed for consultation.

The Nigeria Labour Congress, the organized labor union, opposed the deal, saying it had not been consulted. According to a local newspaper, The Daily Trust, the organization called the deal a “radioactive neoliberal policy initiative” that it said would open Nigeria to “unbridled foreign interference never before witnessed in the history of the country.”

Olusegun Obasanjo, a former president of Nigeria and an elder statesman on the continent, called the Buhari administration’s reluctance “criminal,” according to KTPress, a Rwandan news outlet.

“I am surprised that any African leader at this time would be doubting or debating the benefits of what is going to be signed here and fail to show up,” he said.

Albert Muchanga, the commissioner for trade and industry at the African Union Commission, which oversaw the negotiations, said the 11 holdout countries wanted to hold more consultations at home, and may join later.

“They did not say they are turning their backs on the agreement, no,” he said by telephone from Kigali.

The agreement will come into force after 22 countries ratify it in their national parliaments, which Mr. Muchanga said he expected would happen within the year. Thereafter, countries will be added as they ratify, he said.

Mr. Meservey, the Heritage Foundation analyst, said non-signatory countries may demand exceptions to the general agreement even as the process goes forward.

“My concern about countries holding out is that they are looking for leverage over the final agreement in order to protect their preferred industries,” he said, pointing out that European Union free trade pacts have been plagued by similar problems.

The pact includes a commitment to gradually phase out taxes on imports from other African nations.

Mr. Muchanga said the commision expected the move would bolster small- and medium-sized businesses, better enabling them to contribute to large-scale supply chains.

Intra-African exports now face taxes of 6 percent on average, which African Union officials said makes it more expensive to export goods within the continent than to outside countries.

Only 16 percent of Africa’s trade takes place between countries on the continent, according to the union. The commision expects that to jump to more than 50 percent if all 55 nations sign on to the pact.

Mr. Muchanga said the new agreement also aimed to create jobs and broader economic diversification, in particular by overcoming the continent’s reliance on exporting resources like minerals and oil, and by reducing non-tariff business hurdles, like onerous regulation.

He also said yearly monitoring and evaluation will yield better results for this agreement than for its regional predecessors.

The Economic Community of West African States and the East African Community both have “had a real problem implementing what are very solid agreements,” Mr. Meservey said.

Mr. Campbell of the Council on Foreign Relations said regional cooperation has generally worked better on security issues than on economic ones — for the same reason that the continent’s key players have, for the moment, “hit pause” on the agreement.

“Economic issues hit right in the pocketbook,” he said.