The tie, which was switched to the neutral venue in Nicosia due to ongoing serious unrest in the Ukrainian capital, remained goalless until 10 minutes from time when substitute Eduardo Vargas headed past goalkeeper Olexandr Rybka.
Dynamo were then sucker-punched in stoppage time when Sofiane Feghouli's off-target shot took a wicked deflection off Domagoj Vida which left Rybka stranded.
Rybka, who made a string of fantastic saves in the second half after replacing the injured Olexandr Shovkovskiy, could do nothing to stop either effort.
Dynamo had their chances to take the lead early on at the GSP Stadium, where a minute's silence was held before kick-off for those who have lost their lives in the anti-government protests in Kiev.
Miguel Veloso tested Valencia goalkeeper Diego Alves with a low shot from 25 years but the effort was one of the few the Brazilian would have to deal with.
It was not until after the break that Valencia livened up.
Vargas could have given the Spaniards the lead 65 minutes in after a Jonas cross put the goal on a plate, but a fantastic reaction save from Rybka kept his side in the match.
And it was not long before the goalkeeper was put to the test again as Valenciasensed victory was for the taking.
Rybka made two incredible stops in as many minutes to deny Valencia from going 1-0 up. The first saw him tip Jonas's header from six yards out around the post. Dani Parejo's consequent out-swinging corner found the head of Seydou Keita and it was Rybka once more who stopped the ball from nestling in the back of the net.
But Juan Antonio Pizzi's Valencia were not going to be outdone a third time.
Vargas, who replaced Paco Alcacer with 30 minutes to play, made his side's dominance count and headed beyond the grounded Rybka with 80 minutes on the clock, before Feghouli's deflected effort in the six minutes of added time put the match beyond Dynamo's reach.