Deignan of the Cervelo Test Team finished the 165-kilometre ride from Talavera de la Reina to Avila in a time of four hours, 19 minutes and 14 seconds, finishing three seconds clear of Liquigas rider Roman Kreuziger after the duo had mounted a late breakaway.
Dane Jacob Fugslang was third, 16 seconds behind Deignan, while the main group of riders were around 10 minutes adrift of the winner.
Deignan, 25, moved into the top 10 with Thursday's win, the first by an Irish rider in a Grand Tour since Stephen Roche won a stage of the Tour de France in 1992.
It was on downslope from Boqueron that Deignan made his move, breaking away from the pack along with Kreuziger in an attack that ensured one of the two would be triumphant on the streets of Avila.
Kreuziger was leading the charge in the final straight, but when Deignan pulled out off his back wheel the Czech rider had no response and the Irishman was able to take the victory unchallenged.
On Friday, stage 19 sees the riders go from Avila to La Granja, a distance of around 180km.
