Sergio Camello, an 18-year-old debutant, came off the bench with his side two goals down after Erick Cabaco and Roger Marti struck in the first half and they were soon down to 10 men when Angel Correa was sent off for kicking out at an opponent.
But the league runners-up came roaring back, responding with a scorching long range strike midway through the second half from midfielder Rodri, who is also expected to leave in the summer according to widespread media reports.
Camello then got his chance when a deflected shot bobbled towards him in the area and he calmly struck the ball into the net in the 79th minute. The goal provoked wild celebrations from coach Diego Simeone on the touchline even though the result did not change Atletico's final position in the table.
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Levante, who had clinched survival last week, still could have won the game but Marti could only strike the crossbar from close range, and Atletico ended the campaign second in the standings with 76 points, 10 behind champions Barcelona.
"Of course it was important, we were losing 2-0, Angel was sent off, we made two big mistakes but the team rebuilt itself, and to top it all the goal was scored by a young lad from our academy, by new blood," Simeone told reporters.
"Our young players are making a lot of progress, and not just Camello, all our youth teams are fighting very hard and we have a lot of players with talent and commitment and who excite us and who want to be here."
Captain Godin is leaving Atletico after nine seasons while fellow defenders Filipe Luis and Juanfran have also completed their contracts with the club. Top scorer and highest earner Griezmann announced on Tuesday that he would also be departing, with Barcelona expected to be his next destination.
"I also wanted to pay tribute to our gladiators who are leaving, it's normal for players to leave but we're very proud of them" added Simeone. "Their biggest legacy is not the trophies they have won but their commitment and the respect everyone shows for them. They gave us so much."
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