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.
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.
"I'm of the opinion that he is totally world-class playing in a certain team in a certain way", he told BT Sport.
"I feel sorry for him from that point of view but, as a player, it is frustrating when you watch him because he still looks like a 16 or 17-year-old learning the game".
United go through as runners-up into Monday's draw for the last 16, with Barcelona, Borussia Dortmund, Paris Saint-Germain, Porto, Real Madrid and Bayern Munich their potential opponents in the next round.
Mourinho said his team only improved after he made three changes he "didn't want to make", as Marcus Rashford, who scored United's goal, Jesse Lingard and Ashley Young were all introduced in the second half.
Pogba's tumultuous relationship with Mourinho has been well documented over the past year; the World Cup winner's performances have often been publicly scrutinised by the Portuguese manager.
Sergio Romero, Antonio Valencia, Eric Bailly, Marcos Rojo, Marouane Fellaini, Andreas Pereira, Fred and Pogba were the eight players to come into the starting line-up.
"Today, we played with freshness and bravery, and I'm delighted for them because they have suffered", he said. Not me. I didn't learn anything from this game.
They're world-class players. they've got (Paul) Pogba, (Romelu) Lukaku, (Juan) Mata, (David) de Gea, they've got world-class players. "Nothing surprised me at all".