The referendum was held after debt-ridden Greece and its major international lenders — the European Central Bank, the International Monetary Fund and Eurozone nations — failed to reach a bailout agreement before the previous aid program expired on June 30.
Tuesday's summit was initiated by German Chancellor Angela Merkel and French President Francois Hollande. Both leaders agree that the outcome of the Greek referendum should be respected.
Prior to the summit, the Eurogroup will also hold a meeting on Tuesday to discuss the Greek debt issue.
Italian Prime Minister Matteo Renzi said on Monday that both the upcoming Eurogroup meeting and the emergency Eurozone summit must lead to a definitive solution to the Greek debt crisis.
Niels Annen, a foreign policy spokesman for the Social Democratic Party in the German parliament, has said that Varoufakis' resignation could mean that Athens is open to new proposals.
Greece's total debt currently stands at $350 billion, of which nearly $270 billion is owed to its main international creditors.