Landa was pictured early in the stage by former pro Marco Pinotti riding off the back of the peloton with three Sky teammates supporting him. After 70km Landa was over six minutes behind the pink jersey group.
Sky confirmed that Landa would not complete the race on Twitter, saying the Spaniard was suffering from an illness, presumably picked up on Monday's rest day.
In a later press release, the Sky doctor reported that Landa had viral gastroenteritis.
Sky manager Sir Dave Brailsford said: “Mikel was ill overnight but we spoke this morning and he started today’s stage with the hope of being able to pull through.
"It was pretty clear that the illness had badly affected him and that he wasn't going to be able to continue.
"We are really disappointed for Mikel, who was riding well and looking forward to attacking in the mountains and animating the race.
"However we came here as a team and we’ll continue as a team. There is a long way still to go and, although our focus was on Mikel, there’s plenty of time for us to still make an impact at this Giro.”
Team Sky's bad luck at the Giro continues, with the team still looking to match and better the second-place finish by Rigoberto Uran in 2013.
Last year, on stage 10 as well, Richie Porte's hopes of winning the race were ended when he suffered a puncture and was then handed a time penalty for accepting a wheel of an Orica-GreenEdge rider.
Landa had come into the race on good form, despite missing much of the spring with illness. He won the Giro del Trentino in the run up to the first Grand Tour and sat in eighth place in the classification before today's stage.
Team Sky are now down to seven riders after Elia Viviani missed the time cut on stage eight. Their second best rider in the GC, Nicolas Roche, sits over six minutes down in the standings and it's unclear whether the Irish rider was one who dropped back to help pace Landa back to the pack.
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