As she faced the biggest challenge to her leadership in 12 years in power, Merkel told reporters in Brussels that she thought the accords would suffice for now to placate the hardline rebels within her government.
Overnight, the 28 EU countries agreed a raft of measures including the setting up of secure centres for migrants in the bloc, "disembarkation platforms" in North Africa and sharing out refugees among member states.
Later Merkel announced bilateral accords with Greece and Spain to take back from Germany asylum-seekers who had already registered in their countries.
Merkel's government is hanging in the balance, as she faces a threat by her Interior Minister Horst Seehofer that unless she reaches EU deals allowing the return of many asylum-seekers, he will shutter German borders to them by early July.
Asked whether she thought the accords with Athens and Madrid met Seehofer's ultimatum requirements, Merkel told reporters in Brussels that she believed they even surpassed them.
"They are more than equivalent in their effect," she said.
'Gesture of solidarity'
New Spanish Prime Minister Pedro Sanchez acknowledged that Merkel's difficulties at home had helped focus minds in Brussels.
"We sympathise with the situation Germany is going through at the moment," he told reporters.
"Chancellor Merkel was grateful for this gesture of solidarity."
Seehofer is head of Christian Social Union (CSU), the Bavarian sister party of Merkel's Christian Democrats.
Any move toward closing the border between Bavaria and Austria would force Merkel to sack Seehofer and likely end the parties' seven-decade alliance.
This has raised the spectre of an implosion of Merkel's uneasy coalition government just over 100 days after it took office, and possibly the political demise of the EU's longest-serving leader.
Merkel is to meet with her conservative alliance over the weekend to inform them of the EU summit's results, with announcements expected Sunday on how the two sides will proceed.
The CSU's Alexander Dobrindt sounded a conciliatory note on Friday, saying that the summit's conclusions had gone a long way toward meeting his party's demands.
"The fact is that it is a result of the debate in Germany that the EU is finally confronting the migration issue in a stronger way," he said in Berlin.
'Can't wait forever'
However the party's deputy leader, Angelika Niebler, said the CSU would cast a sceptical eye over the fine print, particularly with regard to implementation of the agreements.
"Are we talking about a few months or a few years?" she told public broadcaster Bayerischer Rundfunk.
"We can't wait forever."
The divide between the sister parties dates back to the height of the refugee influx in 2015, when Merkel, citing the threat of a humanitarian disaster, agreed to leave the border open to asylum-seekers.
Since then, new arrivals have fallen dramatically but the political impact has festered in some quarters and placed particular pressure on conservatives facing deep-seated fears among their voters.
As the CSU gears up for a Bavarian state election in October, it is facing a stiff challenge from the far-right, anti-migration Alternative for Germany (AfD) party.
During the campaign, the CSU has lurched to the right and cranked up its tough talk against migrants, intensifying the pressure on Merkel to harden her stance on an issue that has come to define her politically both at home and abroad.
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