Officers captured the men in the Mendrisio area on Saturday night after the drone, an ADS 95 Ranger, was able to locate them through the use of an infrared camera.
A local woman earlier contacted police about the suspicious individuals south of the city.
Customs border guards, who were operating the drone for their own operations, released it to help in a search for the men, in addition a manhunt on the ground by cantonal and Mendrisio police officers.
The drone was able to locate the men aged 52, 44 and 42 years within 15 minutes, the SDA news agency reported.
One of the men was hiding in the bushes.
The arrested men, residents of Romania, are suspected of being involved in various home burglaries in the region, close to the Italian border.
Known to investigators, they are “strongly suspected of having arrived in Ticino to commit theft”, police said.
The drone is one of 15 operated by the air force in Switzerland.
The aircraft was built by Swiss company RUAG Aviation, based in Emmen in the canton of Lucerne.
Powered by a two-cylinder, two-stroke engine, it has a 5.71-metre wingspan and is capable of flying for four hours at speeds up to 220 kilometres an hour.
Police did not disclose why the border guards were using the drone.
Elsewhere, Neuchâtel cantonal police launched a search for another Romanian man after he broke out of a prison on La Chaux-de-Fonds, either late Friday or early Saturday.
The 40-year-old, who was being detained while waiting to be judged for his alleged involvement in organized gang theft, is believed to have de-activated the prison's security system and used scaffolding erected for renovations to make good his escape.
Police said the escapee is not considered dangerous.