Barring a last-minute disaster, the Australian and Indonesian trade ministers, Senator Birmingham and Enggartiasto Lukita, will finally put pen to paper on Monday morning in the Indonesian capital on the much-delayed deal.

In the short term, Australian farmers – who will see increased annual quotas implemented for live cattle, beef, potatoes and other agricultural exports – will be major beneficiaries.

But ahead of the signing on Monday, Senator Birmingham told The Sydney Morning Herald and The Age the longer-term benefits of the deal for both Indonesians and Australians will flow from Australian universities and healthcare providers being able to more easily operate in Indonesia.

"The chance is there now for Australian universities to forge valued partnerships with Indonesia and become a critical player in supporting the educational empowerment of Indonesia long into the future," he said.

"We have Australian universities in Singapore, Malaysia and numerous other countries. I really hope we see one or more Australian universities open up in Indonesia in the next year or two."

Economists forecast that Indonesia's economy will grow to be the fourth-largest in the world between 2030 and 2040.

Economic growth in Indonesia averages about 5 per cent a year, the country's middle class is growing rapidly and its huge population of 260 million offers a largely untapped market.

At present, the value of two-way trade between Australia and Indonesia is dwarfed by trade with the much smaller markets of New Zealand, Singapore and Malaysia.

The free trade deal, formally known as the Indonesia-Australia Comprehensive Economic Partnership Agreement (IA-CEPA), will allow Australian universities to set up campuses in Indonesia and retain majority ownership of up to 67 per cent, up from the current limit of 40 per cent, a significant concession in a country where economic nationalism and protectionism is still championed by all major political parties.

Senator Birmingham said the "lasting benefits from this agreement will come in time. Services such as education and healthcare providers will have easier access to operate in Indonesia.

"Indonesia is seeing a broad up-tick in its economic potential, its future is strong, and with that will come heightened demand for healthcare and education. So it comes at just the right time for Australian universities and healthcare providers to get in on the ground floor," he said.

More broadly, Senator Birmingham said, deeper engagement and co-operation would benefit the prosperity, security and stability of the entire region.

Though the trade pact still has to be ratified by both country's parliaments, a process that could take months given both nations are about to hold national elections, the signing marks a major milestone and is a win for Prime Minister Scott Morrison after months of uncertainty.

Mr Morrison and President Joko Widodo agreed on the terms of the agreement last September after eight years of negotiations.

But the signing of the deal, pencilled in for November 2018, was derailed after Mr Morrison announced during the Wentworth byelection that Australia would consider moving its embassy in Israel from Tel Aviv to Jerusalem, and extending diplomatic recognition to Jerusalem as Israel's capital.

That proposal drew a furious response from Indonesia, where support for a Palestinian state is widespread, and the signing of the deal was put on ice. Indonesian Foreign Minister Retno Marsudi described the Israel proposal as a slap to Indonesia's face.

Shinta Widjaja Kamdani, the deputy chairwoman of APINDO, the Indonesia Employers Association, summed up her view of the much-delayed agreement succinctly: "Finally we arrived here."

"With the signing on Monday it at least shows that both governments are committed to support the [trade deal]. So, the signing will be good but the ratification is also an important step," she said.

"I think [the deal] brings more the upsides than downsides. I think Indonesia must position itself vis-a-vis other countries because we must be able to compete.''