Diego Alonso blamed Uruguay's World Cup exit on Portugal's last-gasp penalty in their second Group H game.
La Celeste looked on course to reach the knockout stage on Friday with a 2-0 win over Ghana, yet South Korea's late winner against Portugal saw them progress at Uruguay's expense.
Uruguay and South Korea had the same goal difference, but the latter went through courtesy of having scored more goals.
However, Alonso does not think it should have come to that and lamented a contentious late penalty in their 2-0 defeat to Portugal, given against Jose Gimenez for handball.
"We are out because of the penalty that Portugal got and the goals scored," he said.
"We are not out because of the point against South Korea; we are out because of Portugal's penalty that FIFA said was a penalty. It was not a penalty."
1 - Uruguay have failed to qualify for the knockout stages at the #FIFAWorldCup for the first time since 2002, while they had won five consecutive group games in the tournament coming into the 2022 edition. Fallen. pic.twitter.com/zvDTCJArKy— OptaJoe (@OptaJoe) December 2, 2022
Giorgian de Arrascaeta scored twice after Andre Ayew had missed a penalty for Ghana, but it ended in disappointment for Uruguay, with Luis Suarez among those in tears at the full-time whistle.
Despite a disappointing early departure from Qatar 2022, Alonso was full of praise for the way his side acquitted themselves.
"I was critical in the other matches as we missed the creativity," he added.
"The second half against Portugal was really good. Today, I very much liked the team. We found our way, we were brave, not fearful, had the possession, and were able to link up.
"Of course, I would have liked to see this version earlier in the tournament. I have nothing to say to my players because they broke their backs and gave their best.
"Everyone could see what happened to us in the other matches. I know that my players gave it their all.
"From the first day, I believed in my players and they responded on the pitch. I am very proud of what we did.
"Everything we have done was spectacular. I deeply regret we are out, because I truly believe in these players and what we could achieve at this World Cup; their character, their determination."
Alonso bristled at a suggestion from one journalist that his players did not do enough, stating: "I disagree. I can't allow you to say that, I'm very sorry.
"The players made a huge effort every day, every match. They gave their utmost over the last year.
"All the decisions they made in their clubs was based in the national interest. I can't allow you to say they did not break their backs."