The two top diplomats held the meeting at Vienna's Palais Coburg hotel to discuss the progress of nuclear talks between Iran and the Group 5+1 (Russia, China, the US, Britain, France and Germany).
Several other sessions were also held on Thursday concurrently with the meeting between Zarif and Kerry.
In one of them, Deputy Secretary General for the European Union's External Action Service Helga Schmid held talks with Zarif's deputies.
Head of the Atomic Energy Organization of Iran (AEOI) Ali Akbar Salehi and US Energy Secretary Ernest Moniz also discussed details of the technical issues in a long-awaited nuclear deal between Iran and the Group 5+1 (alternatively known as the P+1 or E3+3).
Iran and the six powers have been negotiating over the past 22 months to end more than a decade of standoff over Tehran's civilian nuclear program once and for all.
After missing a self-imposed deadline of June 30 and extra days of tight diplomatic meetings afterwards, the parties decided on Tuesday to continue the talks until Friday in the hope of finalizing the accord.