The act, which a White House spokesman said was meant as common courtesy and not a reflection of policy positions, drew a harsh rebuke from a pair of Republican senators, with John McCain likening it to when British Prime Minister Neville Chamberlain shook hands with Adolf Hitler.
"It just gives Raul some propaganda to continue to prop up his dictatorial regime," McCain, R-Ariz., said of the act.
U.S.-Cuban relations have been in the news recently thanks to the case of Alan Gross, a U.S. Agency for International Development worker who has been jailed in Cuba for four years after the government discovered he helped set up Internet access for a small community of orthodox Jews.
Gross recently released an open letter to Obama seeking his intervention in the case -- and the administration has been criticized for not doing enough to secure Gross' release, The Hill said Tuesday.
Sen. Marco Rubio, R-Fla., who is of Cuban descent, said Obama missed an opportunity to make a point to Castro about human rights while honoring Mandela's legacy.
"If the president was going to shake [Castro's] hand, he should have asked him about those basic freedoms Mandela was associated with that are denied in Cuba," Rubio said.
It was the first time since 2000 a U.S. president shook a Cuban leader's hand -- when Bill Clinton and Fidel Castro shook during a United Nations meeting. Prior to that, the elder Castro had not embraced an American leader since greeting Richard Nixon when he was vice president in 1958.