The prince arrived at Caracas' Maiquetía airport at 5am local time, or 10.30am Spanish time, reported El Mundo.
He was greeted by Venezuela's deputy foreign affairs minister Temir Porras and by the Spanish embassador in Venezuela Antonio Pérez-Hernández.
The welcoming party for the popular prince was rounded out by the Spanish Venezuela's tourism minister Alejandro Fleming.
The charismatic Hugo Chavez died on Tuesday after a long battle with cancer.
His funeral includes representatives from over 50 countries, El Mundo said.
As King Juan Carlos is on sick leave after his recent back operation, Crown Prince Felipe is Spain's acting head of state.
The Spanish government won't be represented at the highest level at Chavez' funeral, as neither prime minister Mariano Rajoy nor foreign minister José Manuel García-Margallo have made the journey.
The foreign minister did not travel because of slight perforation of the eardrum, reported La Vanguardia.
The paper said García-Margallo's doctors had advised the minister not to travel to Venezuela especially given that he had to travel to Brussels on Monday for a meeting with Europe's foreign ministers.
Spain's left-wing groups have, however, criticized the fact that the top tier of Spanish government won't be represented at Chavez' funeral.
Willy Meyer, eurodeputy for the Izquierda Unida (IU) said the decision was "yet another error on the South American front".
Meyer will be attending Chavez' funeral with Spain's federal coordinator for the IU Cayo Lara, reported La Vanguardia.