The Team Sky rider was forced to claw back time after becoming distanced on the steep final ramps of the San Pelaio climb, but eventually crossed the line just 15 seconds back on the stage winner.
That man was once again Julian Alaphilippe, with the Quick-Step Floors rider attacking late and out-sprinting a four man group at the line. A second win in as many days saw the Frenchman extend his race lead out to eight seconds over Primoz Roglic (LottoNL-Jumbo).
Team Sky were active throughout the 166.7km test, with Michal Kwiatkowski and Tao Geoghegan Hart pushing on early out of Zarautz. Jonathan Castroviejo was also involved in the shakeup, with the peloton significantly splitting in half during the day.
A group of 11 riders then formed off the front, with Geoghegan Hart and David Lopez in there representing Team Sky. The group combined well to open out a gap of well over a minute, but as the pace intensified behind that advantage was slashed.
Lopez put in a strong final dig to go clear with 17km to go, but was finally overhauled on the seafront as the final climb began at pace.