Mr Morales travelled to the remote mountain hamlet of La Higuera, where the Argentinian-born veteran of the Cuban revolution was summarily executed on October 9 1967.
“This struggle continues and will continue as long as capitalism and imperialism exist,” he said.
The event was part of a five-day international conference on Che’s anti-imperialist struggle in nearby Vallegrande that concluded yesterday.
Two of Che’s comrades-in-arms from the Bolivian expedition, Brigadier General Harry Villegas — alias Pombo — and Colonel Leonardo Tamayo — alias Urban — travelled to Bolivia for the commemoration.
Che’s children Aleida, Celia, Camilo and Ernesto were also part of the Cuban delegation.
Mr Morales said: “We live in different times, times of democratic liberation.
“Fifty or 60 years ago the struggle was very different — it was with guns, with bullets. Now the struggle is with the conscience and the vote. They are democratic revolutions.”
Gen Villegas, who was also with Che in the Belgian Congo, said: “We came to help a group of young progressives who wanted a different Bolivia, a more equitable Boliva.”
He expressed his deep emotion at returning to the sites “where we gave something of our own lives.”
“Imagine, there was another time when I had to run so, when I had to fight, when I had to kill and when I had to struggle to survive.”
After serving in the government of revolutionary Cuba for several years, in 1965 Che led a guerilla column in a march across the Congo in support of the Simba liberation movement.
In 1966 he led a similar revolutionary expedition against Bolivia’s military dictatorship.
He was shot without trial the day after his capture by troops backed by the US CIA — and allegedly advised by fugitive nazi war criminal Klaus Barbie.
Sergeant Mario Teran, who carried out Che’s execution, later lost his sight to cataracts — only to have it restored by Cuban surgeons in 2006 as part of the continent-wide Mission Miracle programme.