The New Flemish Alliance (N-VA), the largest of the coalition's four parties, had earlier threatened to leave if Michel backed the accord, which has become a cause celebre for European anti-immigration parties.
Belgium's King Philippe accepted the resignations of the N-VA's ministers on Sunday after meeting with Michel at the royal palace, according to a statement.
Michel also presented the king with the list of replacements for the departing N-VA ministers in the interior, finance, defence and migration portfolios.
The departure of the Flemish party means Michel lacks a parliamentary majority five months ahead of legislative elections scheduled for late May.
"I regret that it has come to this," Michel told the RTL-TVI television channel.
He said that a "responsible coalition" had been set up and called for "dialogue with parliament" warning of a looming risk of early elections.
Interior minister and N-VA member Jan Jambon had confirmed earlier Sunday that he and the party's other ministers would step down.
"It's clear," he told national broadcaster RTBF, following hours of uncertainty.
'It's chaos'
In power for four years, the coalition has often been riven over the N-VA's anti-migration positions.
Health Minister Maggie De Block, who will also take on the migration portfolio replacing N-VA's Theo Francken, said she would pursue "a new strict but fair" migration policy.
"I am taking on a department in crisis. It's chaos," the new migration minister said in a statement.
On Saturday night, N-VA leader Bart De Wever warned Michel that the party would leave the coalition if the prime minister flew to a UN conference in Marrakesh on Sunday to endorse the migration pact.
"If we no longer have a voice in this government... there is no point in continuing," De Wever said.
However Michel stood firm, saying he would endorse the pact.
A last-gasp cabinet meeting was held late Saturday, but failed to overcome what Michel called a "profound difference" between the parties.
'Pact with the devil'
The non-binding UN accord, which would promote a common global approach to migrant flows, was initially supported by all four parties in Belgium's coalition.
But the N-VA changed its mind in late October.
The crisis had been rumbling for several weeks before bursting into the open on Tuesday when Michel turned to parliament after failing to unite his government behind the pact.
The liberal prime minister has steadfastly defended the pact, saying on Sunday that it presented "the opportunity for better European and international cooperation".
On Thursday, a majority of parliament supported the accord, but the N-VA and far-right Vlaams Belang party voted against.
French far-right leader Marine Le Pen and Steve Bannon, a former advisor to US President Donald Trump, denounced the pact at an event hosted by Vlaams Belang in Brussels on Saturday.
"The country that signs the pact obviously signs a pact with the devil," Le Pen said.
The draft UN accord lays down 23 objectives to open up legal migration and better manage a global flow of 250 million people, three percent of the world population.
The United States dropped out of talks on the pact last year and countries including Italy, Hungary, Austria, Poland, Bulgaria, Slovakia and Australia have rejected it.
The deal is expected to be ratified at the UN headquarters in New York on December 19.
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