While one of the victims 40-year-old Sridhar Natarajan was working with a pharma firm, the boy Paramshu Jain was the son of a manager of the local Bank of Baroda branch, spokesperson in the Ministry of External Affairs said.
Four Indians, including two women and a girl, were injured in the attack and are receiving medical treatment, the spokesperson said.
India's mission in Nairboi is in touch with the families of the deceased, the spokesperson said.
Masked gunmen had yesterday stormed the packed shopping mall, killing 39 people and wounding dozens others.
Somalia's Al Qaeda-inspired Shebab rebels said the carnage was in direct retaliation for Kenya's military intervention in Somalia, where African Union troops are battling the Islamists.
Senior police sources had described the attackers as a well-organised "terror gang" numbering around 10. The mall, popular with wealthy Kenyans and expatriates and part Israeli-owned, was packed with around 1,000 shoppers when it was attacked.