The forward has only played 12 minutes of football - which came at Manchester United last week - since March 18, and dropping down the pecking order has led to speculation regarding his future.
Jimenez's five-year stay at Wolves is expected to come to an end this summer, with supporters anticipating an opportunity to say goodbye to one of the best forwards in the club's history.
However, despite the Mexican's song being sang numerous times during Saturday's Premier League fixture versus Everton, Lopetegui instead opted to use Matheus Cunha with his final substitutions in the 88th minute.
Jimenez reacted angrily, throwing his shirt into the dugout, applauding the fans and making his way down the tunnel before nine minutes of added-on time were signalled.
After the game, the 32-year-old - who has contributed 57 goals and 24 assists from 165 appearances - returned to the pitch to take part in the end-of-season awards and a lap of appreciation, where he was visibly distraught as he appeared to wave goodbye to supporters.
When quizzed on the matter, Lopetegui insisted that he was not there to 'hand out gifts', but acknowledged that he should have shown more understanding to the situation on an emotional level.
The Spaniard said at a press conference, as quoted by the Express & Star: "He has not been in his best fitness. We put him on in Manchester. Today, with this kind of match, I tried to choose and maybe I can do better as a coach and put him on the pitch for the last ten minutes.
"But it is not a gift for him. He has been a very important player here and I hope he continues to be. But I don't know what is going to happen with him and other players."
"Sometimes you can't make all the things perfect as a coach. You have to fight to win, you have to respect the competition and show the other teams you want to win because maybe you could be in the same position another year.
"You have to be professional (as a coach) and, after, you have to take an emotional decision. So, maybe with this situation, maybe I can do a little bit better as a coach. I am critical of myself."
Jonny and Joao Moutinho - other players who find themselves in similar situations - were not included in the squad, while Ruben Neves again appeared to signal goodbye to the Wolves supporters in the event that a transfer to a Champions League club materialises in the summer.
The game itself ended in a 1-1 draw, Yerry Mina netting a 100th-minute equaliser after Hwang Hee-chan had put Wolves ahead in the first half.