The La Liga outfit made a losing start to their UEFA Champions League campaign as Alex Teixeira's second-half brace led the Ukrainians to victory in the Group A clash in Spain.
Prieto said his team were punished for failing to take their opportunities as he rued their poor performance after the interval.
"In the first half we were the superior team but we didn't score and in the second we paid for that," the 30-year-old midfielder told reporters.
"In the second half the team fell apart and we paid for the way in which we played."
Real Sociedad will be looking to end their three-match winless run when they host Malaga in La Liga on Saturday.
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