The match at Vicente Calderon Stadium on Saturday night appeared to be a mismatch on paper, as the Valencia side sits at the bottom of the table with just 11 points while the 2013-2014 champions came into the contest in second place with 38 points, just one fewer than Barcelona, reports Efe.
Atletico dominated the possession battle, but as has occurred on numerous other occasions this season it had trouble breaking down a well organised defense.
That changed thanks to Thomas, who saved the day for the Colchoneros with his play over the final 20 minutes.
After coming on in the 72nd minute as a substitute for Colombian striker Jackson Martinez, the defensive midfielder -- a key contributor in limited action this season -- drove through Levante's defense and got off a shot that goalkeeper Diego Mariño inadvertently knocked over the line while trying to corral the ball.
The goal averted what would have been a bitter outcome for Atletico, which took the field just a couple of hours after FC Barcelona opened the door for the Madrid side by playing to a scoreless draw in the Catalan derby against Espanyol.
"Once again today, the changes gave us the leap in quality the game required ... (Thomas) is a player who brings fluidity to our team's play and is good at penetrating the area," Atletico Madrid's head coach Diego Simeone said.
With the win, the Colchoneros now lead the La Liga standings with 41 points, two ahead of Barcelona and five clear of Real Madrid, who take on Valencia on Sunday at the Mestalla Stadium.