It will be Nannini’s second year of single-seater racing after a successful 2019 season, during which he won the UAE F4 Championship and scored a best finish of sixth in a part-campaign in the Formula Regional European series.
He also made a one-off appearance in the Renault Eurocup finale last year, bagging a fifth-place finish.
The 16-year-old will be joined at Jenzer by Australian racer Calan Williams and a yet-to-be-named third driver.
“I did tests with Jenzer Motorsport before the season and I'm looking forward to continuing my racing career with this great team.
“I know that the level of championship is very high. Most tracks are new to me. But I'm pretty confident that I can still do well."
Jenzer finished seventh in the teams’ championship in the inaugural FIA F3 season last year, with one victory and two further podium finishes - all courtesy of Yuki Tsunoda, who is stepping up to F2 with Carlin this season.
"Working with Matteo in the test showed us its great potential,” team principal Andreas Jenzer said. "We are very happy to have him in our FIA F3 team and look forward to a great season together."
The 2020 F3 season begins in Bahrain on March 20-22.