White House aide Ben Rhodes told reporters the two exchanged no words more substantive than a greeting.
The Cuban government said the gesture may show the “beginning of the end of the US aggressions”.
The US broke off diplomatic ties with Cuba in 1961 as Fidel Castro aligned with the Soviet Union in the Cold War.
And on Tuesday after the handshake, a White House official said the Obama administration still had grave concerns about human rights violations in Cuba, Reuters reported.
Republicans on Capitol Hill were quick to condemn the gesture, with one Republican congresswoman chiding the move during a unrelated hearing on Tuesday.
“Sometimes a handshake is just a handshake, but when the leader of the free world shakes the bloody hand of a ruthless dictator like Raul Castro, it becomes a propaganda coup for the tyrant,” Florida Congresswoman Ileana Ros-Lehtinen, who is known for her opposition to the Castro government, told Secretary of State John Kerry.
“Could you please tell the Cuban people living under that repressive regime that, a handshake notwithstanding, the US policy toward the cruel and sadistic Cuban dictatorship has not weakened.”
Gradual thaw disrupted
The last US president to shake a Cuban leader’s hand was President Bill Clinton, who greeted President Fidel Castro, Raul’s brother and predecessor, at a 2000 UN General Assembly meeting.
Under President Obama, the US has eased restrictions on Cuban-Americans travelling to the island and on remittances between family members across the two countries0