The duo ditched the rest of the 14-man breakaway that had a yawning gap to the race leader's group with over 50km still to race and looked set to contest a two-up sprint for the stage honours.
But Padun had the misfortune of puncturing on a cold, wet, rainy descent with 24km to go and, despite a quick bike change and a concerted chase, the Ukrainian eventually conceded the stage to the rider from Ecuador.
João Almeida (Deceuninck-QuickStep) once again held onto his 34-second general classification lead over Wilco Kelderman (Sunweb), and 43 seconds over Pello Bilbao (Bahrain McLaren).
Watch the stage 12 highlights from the Giro d'Italia above.
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