Dozens of vehicles entered the capital before dawn, rolling past major landmarks including the Eiffel Tower and the Arc de Triomphe.
The action was organised by the Coordination Rurale union, which says the agreement would expose French farmers to unfair competition from cheaper imports from South America.
Protesters fear that products from Brazil, Argentina, Paraguay and Uruguay would be produced under lower environmental and social standards, putting pressure on local incomes.
The convoys moved slowly through the city but remained peaceful. Police monitored the routes and no major incidents were reported. The demonstration comes as EU leaders weigh whether to finalise the deal, with farming groups urging France to block it.