With first-place Juventus losing 2-1 at Young Boys, United could have jumped above the Italian team in Group H with a win at the Mestalla but manager Jose Mourinho's decision to play a virtual reserve lineup backfired.
Valencia secured a place in the last 32 of the Europa League by finishing third in the group — and it was mainly thanks to Jones. The center back slid in to clear the ball as he chased down Valencia striker Michy Batshuayi, but only succeeded in slotting it past Sergio Romero from 20 meters with the goalkeeper having come off his line.
That made it 2-0 for Valencia in the 47th minute, after Carlos Soler put the home side in front with a driven first-time finish after latching onto Jones' clearing header in the 17th. Substitute Marcus Rashford pulled a goal back in the 87th for United, which had sealed qualification for the knockout stage with a game to spare.
"I think that to qualify in this group is a success," Mourinho said. "Never a failure. To finish second in this group is always a success. "Before the game, I told the players that if we win tonight and Juventus win, we did our job. If we don't win and Juventus doesn't win, we can blame ourselves."
Mourinho said he didn't think the draw for the last 16 would be "significantly different" by finishing first or second. However, United is now assured of playing either Barcelona, Real Madrid, Bayern Munich, Borussia Dortmund, Porto or Paris Saint-Germain.
Paul Pogba, France's World Cup-winning midfielder, has fallen out of favor with Mourinho and started on the bench for the last two Premier League games. He was recalled for the game against Valencia but didn't improve his chances of retaining a place in the starting lineup for Sunday's league game at Liverpool, United's great rival.
Pogba missed a great chance when the score was 0-0, prodding the ball wide from inside the six-yard box following Marouane Fellaini's header at a corner. Pogba failed to shine once again, while Eric Bailly and Andreas Pereira also struggled to make an impact.
Asked if he had learned anything about his players, Mourinho said: "No, maybe you did. Not me. I didn't learn anything from this game. Anything. Nothing that happened surprised me at all." It was a cutting response from Mourinho, who said Nemanja Matic and David De Gea were the only players rested for the trip to Spain.
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