The envoy, Deepak Mittal, met Sher Mohammad Abbas Stanekzai, the head of the Taliban's Political Office in Doha at the request of the Taliban, the foreign ministry said.
India has long had concerns about the Taliban because of their close ties to arch rival Pakistan. The foreign ministry said the two sides discussed the safety of Indians left behind in Afghanistan.
"Discussions focused on safety, security and early return of Indian nationals stranded in Afghanistan. The travel of Afghan nationals, especially minorities, who wish to visit to India also came up," read the statement issued by Indian foreign ministry.
Mittal also conveyed India's fears that anti-India militants could use Afghanistan's soil to mount attacks, the foreign ministry said.
The Taliban representative assured the ambassador that these issues would be positively addressed, it added.
The talks come days after Stanekzai was quoted in the local press as saying that the Taliban wanted political and economic ties with India.
There was no immediate comment from the Taliban on the talks with the Indians.
India invested more than $3 billion in development work in Afghanistan and had built close ties with the US-backed Kabul government. But with the rapid advance of the Taliban, the Indian government was facing criticism at home for not opening a channel of communication to the militants.
In June, informal contacts were established with Taliban political leaders in Doha, government sources said. The big fear is that indigenous groups fighting against Indian occupation in Indian Illegally Occupied Jammu and Kashmir(IIOJK) will become emboldened with the victory of the Taliban over foreign forces, one of the sources said.
"Ambassador Mittal raised India's concern that Afghanistan's soil should not be used for anti-Indian activities and terrorism in any manner," the foreign ministry said.
Stanekzai, who Indian officials say received training in an Indian military academy as an Afghan officer in the 1980s, had informally reached out to India last month, asking it not to shut down its embassy, the source said.