Paolo Tiralongo, 37, won the stage after overhauling Tom Jelte Slagter with a late charge at the end of the 215km ride from Benevento to San Giorgio del Sanno.
Contador, who has worn the pink jersey since Wednesday's fifth stage but dislocated his shoulder in a crash on Thursday, had his lead over Aru cut from four to three seconds with Australian Richie Porte a further 22 seconds behind in third.
The trio crossed the line around 35 seconds behind Tiralongo having raced together for the second half of the stage, but Aru staged a late sprint which shaved one second of the Spaniard's overall lead.
Dutchman Slagter attacked with 60km to go and opened up a lead of nearly two minutes over the chasing group.
However, Tiralongo, who himself broke clear of the chasing group with around 16km left, caught Slagter with just under eight km remaining.
The Italian attacked again with four km to go and charged clear to win the stage by 10 seconds for the third Giro stage win of his career. Slagter finished in seventh.
(Writing by Brian Homewood in Berne; Editing by Douglas Beattie)
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