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The advance resumes: fall of Humaitá

As the Brazilian army was ready for combat, Caxias sought to encircle Humaitá and force its capitulation by siege. To aid the war effort, Caxias used observation balloons to gather information of the enemy lines. With the 3rd Corps ready for combat, the Allied army started its flanking march around Humaitá on 22 July. The march to outflank the left-wing of the Paraguayan fortifications constituted the basis of Caxias' tactics. He wanted to bypass the Paraguayan strongholds, cut the connections between Asunción and Humaitá and finally encircle the Paraguayans. The 2nd Corps was stationed in Tuyutí, while the 1st corps and the newly created 3rd Corps were used by Caxias to encircle Humaitá. President Mitre returned from Argentina and re-assumed overall command on 1 August. With the capture on 2 November by Brazilians troops of the Paraguayan position of Tahí, at the shores of the river, Humaitá would become isolated from the rest of the country by land.

The combined Brazilian–Argentine–Uruguayan army continued advancing north through hostile territory to surround Humaitá. The Allied force advanced to San Solano on the 29th and Tayi on 2 November, isolating Humaitá from Asunción. Before dawn on 3 November, Solano López reacted by ordering the attack on the rearguard of the allies in the Second Battle of Tuyutí.

The Paraguayans, commanded by general Bernardino Caballero breached the Argentine lines, causing enormous damage to the Allied camp and successfully capturing weapons and supplies, very needed by López for the war effort. Only thanks to the intervention of Porto Alegre and his troops, the Allied army recovered. During the Second Battle of Tuyutí, Porto Alegre fought with his saber in hand-to-hand combat and lost two horses. In this battle, the Paraguayans lost over 2,500 men, while the allies had just over 500 casualties.

By 1867, Paraguay had lost 60,000 men to battle casualties, injuries, or disease. Due to the growing manpower shortage, López conscripted another 60,000 soldiers from slaves and children. Women were entrusted with all support functions alongside the soldiers. Many Paraguayan soldiers went into battle without shoes or uniforms. López enforced the strictest discipline, executing even his two brothers and two brothers-in-law for alleged defeatism.

By December 1867, there were 45,791 Brazilians, 6,000 Argentines and 500 Uruguayans at the front. After the death of Argentine vice president Marcos Paz, Mitre relinquished his position for the second and final time on 14 January 1868. Allied representatives in Buenos Aires abolished the position of Allied commander-in-chief on 3 October, although the Marquess of Caxias continued to fill the role of Brazilian supreme commander.

On 19 February, Brazilian ironclads successfully made a passage up the Paraguay River under heavy fire, gaining full control of the river and isolating Humaitá from resupply by water. Humaitá fell on 25 July 1868, after a long siege.

López with the bulk of his army escaped from the siege of Humaitá. Before doing so he tried a daring manoeuvre: to capture on or more allied ironclads by human wave boarding tactics.

The assault on the warships Lima Barros and Cabral was a naval action that took place in the early hours of 2 March 1868, when Paraguayan canoes, joined two by two, disguised with branches and manned by 50 soldiers each, approached the ironclads Lima Barros and Cabral. The Imperial Fleet, which had already achieved the Passage of Humaitá, was anchored in the Paraguay river, before the Taji stronghold near Humaitá.

Taking advantage of the dense darkness of the night and the hyacinths that descended on the current, a squadron of canoes covered by branches and foliage and tied two by two, crewed by 1,500 Paraguayans armed with machetes, hatchets and approaching swords, went to approach Cabral and Lima Barros. The fighting continued until dawn when the warships Brasil, Herval, Mariz e Barros and Silvado approached and shot the Paraguayans, who gave up the attack, losing 400 men and 14 canoes.