Bolsonaro blamed the "Once Upon a Time in Hollywood" actor of making donations to nonprofit organizations that, he claims, are behind some of the fires in the Amazon rainforest.
DiCaprio released a statement via Instagram on Saturday that reads: "At this time of crisis for the Amazon, I support the people of Brazil working to save their natural and cultural heritage. They are an amazing, moving and humbling example of the commitment and passion needed to save the environment.
"The future of these irreplaceable ecosystems is at stake and I am proud to stand with the groups protecting them. While worthy of support, we did not fund the organizations targeted.
"I remain committed to supporting the Brazilian indigenous communities, local governments, scientists, educators and general public who are working tirelessly to secure the Amazon for the future of all Brazilians," he concluded.
Bolsonaro told supporters Friday: “DiCaprio is a cool guy, isn’t he? Giving money to set the Amazon on fire.”
DiCaprio’s environmental organization has pledged $5 million to help protect the Amazon after fires destroyed large parts of the rainforest in July and August.
Bolsonaro’s comments follow a police raid at the headquarters of two nonprofit groups in the Amazonian state of Para.
Several volunteer firefighters, who deny wrongdoing, were arrested and later released. Local police say they are being investigated for allegedly igniting fires to obtain funding through nonprofits.
Federal prosecutors say their investigation points to local land-grabbers as primary suspects.
The number of fires in Brazil this year is the highest on record since 2013 and is up by 85 percent from last year, according to several reports. The country's space research center has already detected more than 80,000 fires this year.
Bolsonaro has claimed in the past, without evidence, that the fires were started by nongovernmental organizations in retaliation for his administration's funding cuts.
However, many scientists and critics of Bolsonaro have said that his government's policy of encouraging deforestation has boosted the land clearance that helps fires rage and given people a license to burn the land.
The Associated Press and Fox News' Christopher Carbone, Tyler McCarthy contributed to this report.