Saturday's match marked the final time Antoine Griezmann, Diego Godin and Juanfran are likely to put on the Atletico shirt, but they could do little to prevent their side from falling behind in the first half.
Erick Cabaco gave Levante an early lead and Roger Marti seized on an error at the back from Thomas Partey to double his side's tally.
But the visitors pulled off the comeback, despite having Angel Correa sent off early in the second half, as Rodrigo and substitute Camello found a way through.
Atletico were behind with just six minutes played as Ruben Vezo headed the ball into the six-yard box and Cabaco converted past Antonio Adan, in for the injured Jan Oblak, with an improvised finish.
Koke produced a couple of good stops to thwart Filipe Luis and Griezmann in the space of three minutes, while Godin's downward header bounced off the ground and skimmed the post as the visitors responded strongly.
But a stray pass from Thomas 36 minutes in gifted Levante a second goal, with Roger the player to profit as he charged through and lifted the ball over Adan.
Diego Simeone's day went from bad to worse when Correa was dismissed for kicking out at Chema Rodriguez following a challenge - VAR being used to overrule the referee's initial call to show just a yellow for the incident.
Atletico were given a lifeline 22 minutes from time thanks to Rodrigo's arrowed shot into the top corner of the net, and 18-year-old Camello marked his first appearance in the top flight by slotting home after Koke saw a shot blocked.
What does it mean? Players come and go, but Atleti resolve remains
Two goals down and with a man disadvantage, it would have been easy for Atletico to roll over. This is a Simeone side, though, and that was never going to be the case.
This might be the last time Griezmann, Godin or Juanfran wear the shirt, but Camello's introduction and the resolve they displayed in the second half shows Atleti's fighting spirit is unlikely to change.
Win, lose or draw, second place was the only position Atletico could finish heading into the final day of action, but this point does at least move them to 76 for the season - their joint-lowest return since 2012 - while Levante's final tally of 44 is two short of last term's.
Camello makes huge impact
Brought on at half-time for the ineffective Thomas, Camello made the most of his 45 minutes on the field as he managed three shots - one of those, his first attempt on target of his LaLiga career, beating the impressive Koke from close range.
Simeone tires of Thomas
Thomas lasted just 45 minutes in his final outing of the season, with Simeone replacing him at the interval following his error for Levante's second goal. The midfielder, who has had a mostly positive campaign, also failed to take a few opportunities that fell his way in the first half - including a scuffed shot from eight yards aimed right at Koke.
Key Opta Facts
- Atletico Madrid have only won one of their past eight LaLiga away games against Levante (D3 L4), 0-5 in November 2017.
- Diego Simeone's side are winless in their past three LaLiga games (D2 L1) – their worst winless streak since May 2015 (four).
- No Spanish player has scored more goals in a single LaLiga campaign for Levante than Roger Marti this season (13).
- Only Barcelona (88), Real Madrid (63) and Sevilla (60) have scored more goals in LaLiga this season than Levante (59).
- Atletico have had players sent off five times in LaLiga this season, their record under Diego Simeone (alongside 2017-18).
Levante's campaign is now officially over, but Atletico have pencilled in a post-season friendly with Beitar Jerusalem next Tuesday.