The Italian court ruled that the ban violates international laws in light of the "exceptionally grave and urgent situation due to the protracted stay of the migrants on our boat", Open Arms said in a statement on Wednesday.
On the heels of the announcement, Spain said Thursday it would be willing to take in some of the migrants, who have been stranded in the Mediterranean for nearly two weeks due to the ban imposed by the Italian interior minister.
Since coming to power in June 2018, Salvini has repeatedly taken a hard line against migrants, which has put Rome on a collision course with its European Union partners.
In early August, he signed a decree banning the Open Arms from entering Italy's territorial waters, arguing that the measure was needed to protect public order.
Under the decree, the Open Arms could be slapped with a fine of up to one million euros and its boat seized if it disobeyed.
Free to disembark
Open Arms' founder Oscar Camps said the court decision now allows the 147 migrants on board to disembark in Italy.
"It's a success. International maritime law prevails," Camps said, before adding that in Italy "everyone does not think like Salvini".
The interior minister has vowed to appeal the judge's ruling and on Thursday signed another decree, saying that the Open Arms' behaviour showed its "political objective of bring (migrants) to Italy".
Camps told journalists in Madrid: "We won the appeal which we filed at an administrative court in Italy against the security decree."
Bring down the government
Salvini is trying to bring down the Italian government, so far without success, after last week pulling the plug on the ruling coalition between his League and the Five Star Movement (M5S).
His party has been riding high in opinion polls, largely thanks to his tough anti-migrant policies.
Prime Minister Giuseppe Conte on Wednesday wrote to Salvini and Defence Minister Elisabetta Trenta asking for the minors aboard to be allowed to disembark the rescue ship, Italian media reported.
Many of the migrants, mainly from Africa, are suffering from "very high levels of post-traumatic stress" and anxiety over their future.