Malori, second to Dan Martin in the Tirreno-Adriatico ITT, completed the 14.3km circuit around Crevalcore in 16:14.
That put the former Italian time trial champion 14 seconds quicker than Anton Vorobyev (Katusha) with Moreno Moser (Cannondale) third after a time of 16:32.
Malori's team-mate Diego Ulissi finished sixth in 16:53 to extend his lead on GC, going into Sunday's final stage.
He leads stage three winner Damiano Cunego by 1:35 ahead of the route from Monticelli Terme to Fiorano Modenese.
- Sports & Recreation
- Moreno Moser