Palestinian leader Mahmud Abbas (L), Israel Defence Minister Benny Gantz (AP Photo)
Gantz told Abbas that he intended to "continue to promote actions to strengthen confidence in the economic and civilian fields, as agreed during their last meeting," the ministry statement said.
"The two men discussed security and civil matters," it added.
Israeli media reported that the meeting took place at Gantz's home in the central town of Rosh HaAyin.
In late August, Gantz visited the Palestinian Authority's headquarters in the occupied West Bank city of Ramallah for talks with Abbas, the first official meeting at such a level for several years.
But after those talks, hawkish Prime Minister Naftali Bennett underlined that there was no peace process under way with the Palestinians, "and there won't be one".
Palestinian Civil Affairs Minister Hussein al-Sheikh tweeted on Wednesday that Abbas met with Gantz.
"The meeting dealt with the importance of creating a political horizon that leads to a political solution, in accordance with international resolutions," he said.
The pair also discussed "the tense conditions on the ground due to the practices of settlers" as well as "many security, economic and humanitarian issues".
Israel's right-wing opposition party Likud condemned the latest meeting, saying that "concessions dangerous for Israel's security were only a matter of time".
Likud added a dismissive reference to Bennett's governing coalition, which includes an Israeli Arab party for the first time.
"The Israeli-Palestinian government has put the Palestinians and Abbas back on the agenda... it is dangerous for Israel," Likud said.
Deepens Palestinian divide
Palestinian movement Hamas, which controls the Gaza Strip, also condemned the visit.
It went against the "national spirit of our Palestinian people", a Hamas statement read.
"This behaviour by the leadership of the Palestinian Authority deepens the Palestinian political divide, complicates the Palestinian situation, encourages those in the region who want to normalise relations with the occupier, and weakens the Palestinians' rejection of normalisation," Hamas spokesman Hazem Qassem said.
The Gulf Arab states Bahrain and the United Arab Emirates, as well as Morocco and Sudan, signed US-brokered normalisation deals with Israel during the presidency of Donald Trump.
Relations between Israel and the Palestinians deteriorated sharply during Likud leader Benjamin Netanyahu's record 12 years as prime minister, up to June this year.
US-sponsored peace talks broke down in 2014 as Netanyahu oversaw an intensification of illegal Jewish settlement expansion in the occupied West Bank.
Right-winger Bennett, the former head of a settler lobby group who opposes Palestinian statehood, leads a coalition of parties from the Jewish nationalist right and the left and centre.
Gantz's meeting with Abbas follows a visit to the region by US National Security Adviser Jake Sullivan.
*This story was edited by Ahram Online