Vishwakant Ankit Reddy, in his mid-30s and currently employed with IT major Infosys, and Pushpendu Ghosh are both safe and now in police custody, an External Affairs Ministry spokesperson said. Details of Ghosh were not immediately known.
Initially it was believed that Ankit Reddy was the only Indian hostage.
External Affairs Minister Sushma Swaraj said Prime Minister Narendra Modi was monitoring the hostage situation throughout.
"The hostage crisis in Sydney is over. Vishwakant Ankit Reddy is safe. He is undergoing some medical check ups and will be back home safe," Swaraj said in her first tweet after the end of the dramatic siege.
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"We were in constant touch with our mission in Sydney and the family of Shri Reddy. The PM was monitoring the situation throughout," she said.
Ishwar Reddy, a relieved father of Ankit Reddy, said he received a message from his daugther-in-law as well as his colleagues after his son came out of the popular Lindt cafe.
"My son is okay and my son will call me," he said.
Reddy, a native of Guntur, said his son has been working in Australia for the past seven years.
Shilpa told him that Australian Police met her after her husband was taken hostage and asked her not to worry.
Quoting his daughter-in-law, Ishwar said she has been told the "operation (to free the hostages) will be completed in one day" and was asked not to worry.
"My son left for office in the morning at around 10 and went to the cafe where a gunman took him and 29 others hostage. The hostage-taker closed the cafe. The hostages were also offered food," Ishwar said.
"My son, after completing his studies at BITS Pilani, worked in US and then shifted to Australia after getting a job with Infosys. He returned to India for marriage and has been working in Australia for the past seven years," Ishwar said.
With regard to the gunman's demands, Ishwar said "they are not clear".
Guntur (Urban) Superintendent of Police Rajesh Kumar told PTI that Australian authorities were in touch with Vishwakant Ankireddy's wife. The couple has a 6-year-old daughter.