During his weekly address in St Peter’s Square in the Vatican, the pontiff said the “lung of forests” was “vital” for the health of the planet.
Troops in the world’s largest Catholic country, backed by aircraft, have been deployed to fight the blazes after President Jair Bolsonaro said he was committed to protecting the region.
Around 44,000 military personnel are available for “unprecedented” operations, say officials.
Six states have asked for federal help – Roraima, Rondonia, Tocantins, Para, Acre and Mato Grosso.
The number of forest fires in Brazil since January – more than 74,000 – has increased by 83% compared with the same period last year, with smoke visible from 400 miles in space.
The pontiff, who is from neighbouring Argentina, told the public that “we’re all worried” about the fires, adding: “Let us pray so that, with the efforts of all, they are controlled as quickly as possible.”
The fires have sparked an international outcry because of the Amazon’s key role in combating global warming, with the forests absorbing carbon dioxide from the air.
Francis, who wrote a major document in 2015 on protecting the environment, has defended the rights of the Amazon’s indigenous population to keep their lands and protect their cultures.
He has also called for a reduction in the use of fossil fuels.
Mr Bolsonaro has been attacked by critics who claim the fires were a result of his plans to develop the Amazon and allow mining and commercial agriculture on protected indigenous reserves.
Environmentalists say the evidence shows this crisis is man-made – some fires may have been started accidentally but many will have been deliberately set.
Farmers have burned parts of the forest through a process called “slash and burn”, in which they cut down trees and set them alight to clear room to grow crops and raise livestock.
French President Emmanuel Macron has called the blazes an international crisis and tweeted: “Our house is burning. Literally. The Amazon rainforest – the lungs which produce 20% of our planet’s oxygen – is on fire.”
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The Brazilian leader hit back at his critics and accused Mr Macron on Twitter of using a “sensationalist tone” that “does nothing to solve the problem”.
Mr Bolsonaro has previously described rainforest protections as an obstacle to economic development, sparring with opponents who note the Amazon produces vast amounts of oxygen for the planet.
The Brazilian leader said he wants to convert land for cattle pastures and soybean farms.
He said other countries’ concerns over the widespread blazes revealed a “colonialist mindset”.