The former Liverpool defender flew into Bergamo for his medical yesterday and subsequently signed a one-year contract.
The 34-year-old's deal is reportedly worth €1 million (A$1.67m).
He spent the last three seasons with Fenerbahce in Turkey and brings important experience to Atalanta, who will play UEFA Champions League football for the first time in their history this season.
“I spoke with a few friends who play in Italy and they told me only positive things about Atalanta," the former Slovakia captain said.
"I think finishing third in Serie A, which is a strong competition, you must have real quality.
“I played in the Champions League with Liverpool and I’m happy that I can be part of the tournament again with Atalanta.
"I’m looking forward to it, but also to my Serie A debut, as it’s something new and I can’t wait to be on the pitch.