It began on 3 December 1864. The Brazilian navy, commanded by the Marquis of Tamandaré, sealed the river with a corvette and four gunboats while Colorado forces under Venancio Flores closed in by land. Inside the defensive perimeter, just six blocks by two near the city center, Gómez and his second, Lucas Píriz, had a garrison of around 1,250 men. The attackers fielded thousands and brought thirty cannons, several of them modern rifled guns that could shatter masonry from a distance. From 6 to 8 December the besiegers pushed into the streets and were thrown back. They settled in to wait for reinforcements, and the bombardment ground on, day after day, against a town with no way out.

The defenders held through weeks of shelling, hunger, and exhaustion, hoping for relief that never came. By late December the allied army had grown enormously, joined by Brazil's Army of the South with fresh brigades and the artillery of Lieutenant Colonel Émile Mallet. The fighting turned merciless on both sides. On 31 December the final assault began, and the last battle raged for some fifty-six hours through the rubble of the city. On 2 January 1865 the defenses were overrun. By then much of Paysandú lay in ruins, and the basilica that had sheltered civilians was gutted. The townspeople who survived had endured a month most could scarcely have imagined.

What happened to Leandro Gómez turned a defeat into a martyrdom. Captured after the city fell, he was offered guarantees for his life. They were not honored. On the orders of the Colorado colonel Gregorio "Goyo" Suárez, Gómez and several of his officers were shot in the street. Suárez had personal scores to settle, and the killings were as much vengeance as war. The brutality only deepened the legend. In the decades that followed, Uruguayan historians, poets, and balladeers told and retold the defense of Paysandú until it became a shared inheritance, a story that stood above the country's bitter party divisions. The men who died here were not statistics. They were defenders who chose to stay, and a city that paid for their choice.