
Italian Di Giannantonio, who won the Catalan MotoGP last time out, clocked a top time of one minute 44.808 seconds at the Mugello circuit, 0.91sec ahead of countryman Francesco Bagnaia.
The 27-year-old rides for Ducati satellite team VR46 and was one of four Italians in the top four alongside former world champion Bagnaia, Enea Bastianini and Franco Morbidelli.
He was also fastest in the morning’s free practice which has no bearing on Saturday’s qualifying sessions.
Di Giannantonio currently sits 26 points behind championship leader Marco Bezzecchi ahead of qualifying and the Sprint race on Saturday, and Sunday’s Grand Prix.
Marc Marquez was sixth fastest after being cleared to compete despite suffering a broken foot in a spectacular crash at the French MotoGP earlier this month.
The injury kept him out of the main race at Le Mans as well as the last race weekend in Barcelona where his brother Alex Marquez suffered a horrific crash which keeps him out of the grand prix in Italy and Hungary.