Nolito scored a first-half hat-trick for the La Liga side, who had trailed early at Prenton Park after an Aiden McGeady strike on Wednesday.
It saw Everton's winless pre-season continue, results which are worrying ahead of their Premier League opener against Leicester City on August 16.
Despite the loss, Martinez was pleased with his side's tempo and physicality.
"It was a tough test," he told evertontv.
"It was one of those exercises where we got the benefit of testing different things and seeing the fitness levels of the players.
"They played as we expected. They pressed us really high up and we wanted to take advantage of that and make sure we could test them.
"We gave a couple of goals away, which is something we need to shape and polish and use as an advantage.
"All in all, I thought the tempo and physicality was really consistent through the 90 minutes and sometimes it's difficult to get that in a pre-season friendly."
Tim Howard, Leighton Baines, Sylvain Distin, John Stones, Gareth Barry, James McCarthy, Steven Naismith, Ross Barkley and Leon Osman all started.
New signing Muhamed Besic came off the bench, as did Darron Gibson, while Phil Jagielka and Steven Pienaar sat out.
Martinez said Jagielka and Pienaar would be ready for Saturday's clash against Paderborn.
"Phil and Stevie were involved on Sunday at Goodison and it was always the plan to work through the week and make sure they are ready for the game in Germany," he said.
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