The state capture commission heard last year how the Guptas had a hand in the closing down of the SAA route between Johannesburg and Mumbai in 2015.
Ramaphosa said SAA's loss of the Mumbai route "was part of how we lost our way".
"Our South African Airways is going through troubling times at the moment," he said. We want nothing better than to see South African Airways have direct flights to India once again."
He added: "If that is one of your dreams, we will fulfil it."
Public enterprises minister Pravin Gordhan told the media in New Delhi that work would begin on reinstating the route.
"There was a direct route [and] it was stolen from SA," he said.
Gordhan acknowledged that despite interest by Indians in investing in SA and partnering with state-owned entities, there is cleaning up to do.
"We have to focus on getting SAA into shape and make sure it's profitable," he said.
Embattled state-owned power utility Eskom also came up as a matter of concern, with Indian companies worried about power security.
"We know that the inability of Eskom to deliver good electricity is a threat to the economy and I am sure it is a threat to your businesses, and it's also something that tends to turn those who want to invest in SA away," Ramaphosa said.
His visit to India was widely lauded by government and business leaders, who are optimistic about relations between the two emerging economies.