Los Franjirojos poured it on in the second half as Nacho, Piti and Franco Vázquez scored after the break.
With 25 points the Rayistas now trail Levante by two points for the final Europa League spot in sixth.
Piti took five shots and completed 21 passes - six to Roberto Trashorras.
Rayo Vallecano were able to convert their 66.9% possession rate into a victory.
Franjirojos produced 18 shots, including seven on target, while also drawing 17 free kicks and three corners. They also completed 393 passes and had 27 crosses in the win.
Andrija Delibasic made the biggest impact of any Rayo Vallecano substitute after coming on for Lass in the 73rd minute as he took two shots.
Leo had five shots for Rayo Vallecano, more than any of his team-mates.
Alejandro Gálvez's 20 passes to Jordi Amat were the most of any Rayo Vallecano team-mates.
Levante had 33.1% of the possession during the loss.
Levante had nine shots, including three on target.
Ángel made a big difference on the match for Los Granotes after coming on for Míchel in the 63rd minute, as he took two shots.
The three attempts by Barkero were the most of any Levante player.