Already assured of knockout phase Champions League football next year, the Manchester United boss made eight changes for Wednesday's match at Valencia as injuries took their toll ahead of the trip to Liverpool.
United knew victory at the Mestalla would see them top Group H in the unlikely event that Juventus slipped up in Switzerland, but Mourinho's men failed to do their bit as the improbable played out at Young Boys.
The Serie A giants lost 2-1 at the same time that United fell by the same scoreline in Spain, where a Carlos Soler strike and Phil Jones own goal meant substitute Marcus Rashford's late strike was just a consolation effort.
"I think that to qualify in this group is a success," the United boss 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.
"I don't think the draw finishing first or second - apart from a couple of clubs that are clearly much better than the others - I don't think the draw will be significantly different.
"But I expect (better) from my players, especially players that week in, week out, you ask me 'why don't they play?', 'why don't they start?'
"(It) was a good match to play, a match without any kind of pressure, a match in a competition that everybody likes to play. "And, in the end, my team improved, really, when I made the changes that I didn't want to make, which is a little bit of frustration because I didn't want to play the three players that I played in the second half."