He still leads by two seconds in the general classification but struggled to pull on the Maglia Rosa at the presentation.
His Tinkoff-Saxo team said Contador, who also hurt his right knee, had a 30-minute medical examination following the conclusion of the stage, which included undergoing x-rays.
"I haven’t broken anything but I have suffered a dislocation of the left shoulder," Contador said in a statement.
"The doctors have recommended that I immobilize my left arm during the evening and night, while I try to move it a bit with the help of my other arm to promote the movement of the shoulder.
"I will focus on this until tomorrow before the stage, where the doctors will come back to put on a layer of bandage for the race.
"I will try to start tomorrow on stage seven, as I have worked very hard ahead of the Giro. I will try to continue until the very last moment. I’m optimistic about the start tomorrow, but we have to wait until right before the start to see what happens and how serious the effect of the crash is.”
Friday's 264km seventh stage is the longest in this year's race.
Italy's Daniele Colli (Nippo-Vini Fantini) will not be continuing after his team confirmed he had broken his arm in the crash which took down a sizeable chunk of the peloton as it roared towards the finish line.
Earlier on a relatively flat stage featuring just one categorised climb a five-man break was caught with 14km remaining with Contador's team and the Astana outfit doing most of the work on the front.
Greg Henderson positioned team mate Greipel perfectly on the front with 200m to go and the German veteran did the rest, pumping hard to the line to maintain his record of winning at least one stage in every Giro has he ridden.
Contador's main rivals for victory all came through unscathed with Astana's Fabio Aru and Team Sky's Richie Porte avoiding any mishaps to stay in the hunt.
(Reporting by Martyn Herman; editing by Justin Palmer and Pritha Sarkar)
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