The home side looked set to drop points in Sunday's match after conceding twice inside the opening 20 minutes of a home league game under Diego Simeone for the first time, with Charles and Anaitz Arbilla defying the form book at the Wanda Metropolitano.
Joao Felix scored his first LaLiga goal to start the comeback before the half-hour and Vitolo, introduced at the interval, dragged his side back onto level terms early in the second half against an Eibar side still without a win this season.
Los Rojiblancos carved out 1-0 victories over Getafe and Leganes in their initial matches and they showed true fighting spirit as Thomas poked home to lift Atletico above Athletic Bilbao and Sevilla to the top of LaLiga.
1 - Atletico de Madrid have won a game they were trailing in by two goals for the first time since May 2009 in LaLiga, with that occasion being a 3-2 victory over Espanyol. Suffering. pic.twitter.com/C8HEhJDoVO— OptaJose (@OptaJose) September 1, 2019
Charles converted Fabian Orellana's cross on the counter to give Eibar a seventh-minute lead and, after Diego Costa fired over the bar from close range, Arbilla doubled his side's tally with 19 minutes played.
The left-back's powerful shot took a deflection off Jose Gimenez and Jan Oblak was unable to react.
It did not take long for Simeone's men to respond, though, with Costa showing good strength in the box and returning the pass to Joao Felix for a simple finish into an empty net.
Atletico, who had a penalty appeal rejected before half-time when Joao Felix was seemingly clipped inside the box, brought on Vitolo for Marcos Llorente at the interval and that change proved inspired.
The lively Renan Lodi picked out Vitolo's run and the attacker poked the ball past Marko Dmitrovic to level matters seven minutes into the second half.
It looked like being a day of frustration for Atletico when Costa had two goals ruled out for offside, only for another substitute, Thomas, to pop up with a dramatic late winner.
What does it mean? Simeone needs to find right system after third narrow win
Simeone reverted to a four-man backline for this match, having operated with wing-backs in the 1-0 win at Leganes last weekend, but Atletico started slowly and were very nearly made to pay come full-time.
Last season's runners-up have been far from free-flowing in all three matches this term, winning each by a one-goal margin. They were bailed out here, though, and Simeone now has a two-week break to find the right system to get the most out of his stellar squad.
Joao Felix up and running
As well as showing incredible fighting spirit to claim all three points, another big positive for Atletico was the partnership between Costa and Joao Felix, with the latter's goal making him the youngest Portuguese player to score in LaLiga in the 21st century at 19 years and 296 days.
Llorente rightly sacrificed
The decision to bring on the more attack-minded Vitolo for Llorente at half-time gave Atleti some added impetus. Llorente attempted an underwhelming 10 passes in the opposition half during his 45 minutes on the field and lost possession four times. It was not the only inspired change made by Simeone, of course, as Thomas popped up with a late winner after coming on for Joao Felix.
Key Opta facts
- Atletico Madrid won a game they were trailing in by two goals for the first time since May 2009 in LaLiga, when they also prevailed 3-2 against Espanyol.
- Atleti have earned six LaLiga points thanks to Thomas' past six goals in the competition: two versus Deportivo La Coruna (November 2017), two against Athletic Bilbao (November 2018) now two at Eibar's expense.
- Vitolo has scored in back-to-back LaLiga games for the first time since November 2016 when playing for Sevilla.
- Charles scored the fastest goal by a visiting player at the Wanda Metropolitano in all competitions after his opener clocked in at six minutes and 41 seconds.
Atletico travel to Real Sociedad in their first match back after the international break on September 14, while Eibar host Espanyol the following day.