Kiryienka finished 28 seconds clear of the field on the 186.5km moutain stage between Burgos and Pena Cabarga as Astana rider Nibali ended 25 seconds adrift of America's Christopher Horner, who finished sixth on the stage and closed to within three seconds of the overall lead.
With Kiryienka well clear of the pack, Horner decided to break away from the group he found himself in and pushed on for the line in an attempt to close the gap and overhaul Nibali.
Although he failed to do so, the gap of just three seconds will give the RadioShack rider plenty of encouragement as the tour enters the final stages.
Spanish duo Alejando Valverde and Joaquim Rodriguez finished two minutes and 13 seconds adrift of Kiryienka and, although they lost time over Horner, remain in third and fourth places respectively.
With just three stages remaining it remains unclear who will end Sunday's final stage in Madrid as the holder of the red jersey, with Horner closing in on Nibali at just the right time.