Sequeira was lauded at the annual ceremony in London for his shockingly raw footage of the violent crackdown against protesters in Nicaragua that began last year and continued into 2019.
His work showed demonstrators' arrests and clashes with security forces after protests erupted on April 18, 2018, in response to President Daniel Ortega's social security reforms.
The resulting bloodshed has seen 325 people killed, from both the opposition and security forces, another 2,000 injured while 60,000 inhabitants have fled into exile, according to human rights groups.
"This award is for the Nicaraguan people who have fought for democracy," Sequeira said after being handed the award by Nicaraguan rights activist Bianca Jagger.
"(It's) pretty hard to work in that kind of environment, with a repressive regime, when you are followed by people you don't know all the time."
Sequeira, 25, started shooting video at the age of 17 and has worked for Telemundo, RCN, HBO, Reuters and Rutly.
He has covered events across the Americas, in Europe and Asia, as well as in the Middle East.
His work has included reporting on the plight of the Kurdish people, the jihadist attacks in Paris in 2015 and the terrorist attacks in Orlando, Florida in 2016.
Sequeira has been working for AFP since 2018.
"This award represents a new success for AFPTV's coverage in Latin America, where AFP has developed a highly talented network to provide a view, and understanding, of the continent's news to the rest of the world," said Phil Chetwynd, AFP's global news director, at the award ceremony.
This is the fourth time in six years that an AFP journalist has won the prize.
It was launched in 1995 in memory of the independent videographer Rory Peck, who was killed in Moscow two years earlier.
The award recognises the best independent news cameramen, and the ceremony is one of the main ways that the Rory Peck Trust, which administers the prize, raises funds to assist freelance journalists.
In its 24th year, the 2019 award was presented by Sudanese journalist Nima Elbagir, and Alex Thomson, a British journalist for Channel 4 News.