Austin's two-day visit marks the first by a US official since President Joe Biden's inauguration in January.
Following a meeting between the two diplomats on Sunday, Austin thanked Gantz for the "important discussions on the regional threat environment and ways to deepen US-Israel defense cooperation".
"I'm committed to continuing our close consultations on threats posed by Iran and to strengthening Israel's security," he added.
In response, Gantz said: "We will continue to work with the US to ensure that any agreement with Iran safeguards the vital interests of the international community and protects Israel.
"Secretary Austin and I agreed to continue a close dialogue on the urgent security challenges in the region.
"Israel sees the US as a full partner on all operational fronts - the first of which is Iran"Grateful to share vision and goals with our strategic partner and friend and know that we will work together to make sure that any Iranian nuclear agreement protects the vital security interests of the international community and of Israel."
Austin is also expected to meet Prime Minister Benjamin Netanyahu.
The Defence Secretary is not expected to visit the Palestinian Territories, although Biden has signalled that he wants to rebuild ties with the Palestinians.
The previous administration of Donald Trump made several major diplomatic moves which were welcomed by Israel but denigrated by the Palestinians, including moving the US embassy to Jerusalem, and weakening support for a two-state solution.
Austin is expected in Germany on Tuesday, and in Brussels after that.