The Irishman was 78th across the line and dropped down to 30th overall and is now 44:22 down on new race leader Joaquim Rodriguez (Katusha).
The Spanish rider entered the stage one second adrift of overnight leader Fabio Aru (Astana) but when the latter crossed the line two seconds adrift of Rodriguez he lost the race leader’s red jersey.
It is now Italian Aru that trails by one second overall, with Rafal Majka (Tinkoff-Saxo) retaining his third place overall at 1:35.
Dutchman Tom Dumoulin (Giant-Alpecin) put in a strong ride to keep his fourth spot at 1:51 on a day Frank Schleck (Trek factory Racing) took one of the biggest results of his career.
The 35-year-old from Luxembourg attacked from the day’s escape group on another brutal mountain stage that featured seven categorised climbs tallying and over 5000 metres of climbing.
Rodolfo Torres (Colombia) was second on the stage with Moreno Moser (Cannondale-Garmin) in third.
Today sees the riders have a rest day before the final four stages.