Hundreds of public buses ferried young and old to the concert site, and the government laid on even more transportation, hoping for a large turnout.
Most concertgoers wore white – to symbolize peace – and some held up signs reading "Peace on Earth" and "We Love You Juanes."
Puerto Rican singer Olga Tanon opened the concert with a loud shout-out to the crowd, packed under a broiling Havana sun.
"Together, we are going to make history," she said as the plaza erupted in cheers.
Juanes came on stage three hours into the show, gazing out at the multitudes in evident disbelief. "I can't believe what I am seeing with my own eyes," he said.
"We came to Cuba for love. We have overcome fear to be with you and we hope that you too can overcome it," Juanes said. "All the young people in the region, from Miami in the United States and in all the cities … should understand the importance of turning hate into love."
He repeated that theme after the concert ended.
"For me, to see more than a million people experiencing happiness, love and peace is incredibly powerful, because what happens in politics is people become divided," Juanes told AP Television News. "With music we are all the same … music is for everybody."
Before the show started, colorful umbrellas sprouted like flowers across the vast square as revelers shaded themselves from the unrelenting sun. Ambulances set up behind the stage treated those felled by dehydration and other ailments, many before a single note was played.
"We are going to stay as long as we have the strength," said Cristina Rodriguez, a 43-year-old nurse accompanied by her teenage son, Felix. They and thousands of others arrived hours before the concert to get a good spot, ignoring government warnings not to turn up until noon.
"We've been here since three in the morning waiting for everyone, waiting for Juanes and for Olga Tanon," said Luisa Maria Canales, an 18-year-old engineering student. "I'm a little tired, but I am more excited."
That excitement did not extend to some across the Florida Straits, where Juanes had endured death threats, CD smashing protests and boycotts since announcing his plan for the "Peace Without Borders" concert in Havana.
Police in Key Biscayne, Florida, said they were are keeping watch over the homes of both the rocker and his manager, Fernan Martinez Maecha.
Still, the criticism from Florida was far from universal. Spanish-language stations covered the event and several exile groups voiced support, describing it as a rare chance for Cubans to get a glimpse of the outside world.
Some Cuban officials used the opportunity to deride U.S. foreign policy toward Cuba, and the 47-year trade embargo in particular. But Juanes insisted the concert was about music, not politics.
"It is one more grain of sand for improving relations through art," the singer said upon arriving in Havana late Friday.
Of the threats from Miami, he said only: "It is a city that I love."
Juanes met recently with U.S. Secretary of State Hillary Rodham Clinton and the concert even prompted comment from President Barack Obama, who told the Spanish-language Univision network that the event probably wouldn't have much effect on U.S.-Cuban relations.
"My understanding is that he's a terrific musician. He puts on a very good concert," Obama said in the interview broadcast Sunday. "I certainly don't think it hurts U.S.-Cuban relations. These kinds of cultural exchanges – I wouldn't overstate the degree that it helps."
The show also featured Cuban folk legend Silvio Rodriguez and salsa stars Los Van Van, as well as performers from Spain, Ecuador, Italy and elsewhere.
The festivities took place below a giant likeness of revolutionary icon Ernesto "Che" Guevara and near the heavily guarded offices of Fidel and Raul Castro.
Juanes, who has won 17 Latin Grammy awards, more than any other artist, is known for his social activism. His first "Peace Without Borders" concert in 2008 drew tens of thousands to the border between Venezuela and Colombia when tensions were high over a Colombian commando raid into neighboring Ecuador that killed a leading Colombian rebel commander.