Prat-Gay's ministry will be split in two, said chief of staff Marcos Pena.
Nicolas Dujovne, a respected economist, will take over as finance minister. Luis Caputo, who previously served Prat-Gay as budget secretary, will take over the newly created budget ministry.
The president himself requested Prat-Gay's resignation, Pena said.
"It's a matter of policy differences," he told a press conference.
It is Macri's first cabinet reshuffle since he swept to power just over a year ago, putting an emphatic end to 12 years of left-wing rule.
Other reforms under his watch included the removal of subsidies for public transportation, electricity and gas, which triggered angry protests.
Macri says the reforms are necessary to revive Latin America's third-largest economy.
But as he starts his second year in office, the promised growth has yet to arrive.
The economy is forecast to shrink by around two percent this year.
Seven in 10 Argentines are worried about the economy, and an equal number think Macri "governs for the rich," according to a recent poll.
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