Valencia eased past a La Liga Osasuna into the quaterfinals, while Malaga flirted with danger against third tier Elbar before a flurry of late goals put them safely into the last eight.
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Valencia will play 2011 winners Real Madrid or Celta Vigo for a place in the semifinals, with Celta holding a 2-1 advantage from last month's last 16, first leg ahead of their visit to the Bernabeu on Wednesday.
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Malaga are facing a probable last-eight clash with holders Barcelona, who host Cordoba on Thursday having won their first leg 2-0 at the second-division Andalusian club.
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Valencia went into their second leg against Pamplona-based Osasuna with a 2-0 lead and were cruising at a half-empty Mestalla when Tino Costa smashed in a free kick to open the scoring in the 34th minute.