Both teams showed intent during the early stages, with Jorge de Frutos and Oscar Rodriguez having a shot apiece blocked inside the opening six minutes.
While Los Franjirrojos were able to begin controlling possession, the hosts did a good job of limiting them as De Frutos headed over on the stretch, Isi Palazon sent an ambitious attempt bouncing harmlessly wide and Andrei Rațiu’s strike was blocked.
There was still a blow for Los Pepineros when Seydouba Cissé went off injured just 23 minutes into proceedings.
The battle continued as Florian Lejeune sustained a cut after clashing heads with Munir El Haddadi, and the temperature rose slightly following Dani Raba’s booking for dissent after the winger thought he was fouled by Isi and Pathe Ciss.
That didn’t translate to goalmouth action but Sergio González had a big chance to at least record the game’s first shot on target, only to turn Raba’s free-kick delivery harmlessly wide.
The Leganes captain was then sent off for grabbing Randy Nteka while he was the last man, although there was no further punishment for the hosts as Lejeune blazed his shot high and wide.
Rayo stepped things up after the restart and a last-ditch intervention from Jorge Sáenz was required to deflect Nteka’s shot wide, which contributed to their steadily increasing corner count. It looked as though there would be an opening when Alvaro Garcia’s cross found Lejeune, but Sáenz made another vital block and scrambled the ball away.
The game’s first shots on target eventually came in the 78th minute and proved to be worth the wait for Los Franjirrojos, as Lejeune headed onto the crossbar from an Isi corner and Ciss saw his own header saved before turning in the rebound.
With the game almost up, Darko Brasanac won a penalty from Lejeune in the final seconds, and after Miguel de la Fuente was denied by Augusto Batalla, the ball was kept alive and Valentin Rosier poked it in.
That was ruled out due to the Frenchman encroaching, and Batalla outfoxed De la Fuente again to deny the retaken effort and dramatically earn all three points in Rayo’s seventh consecutive match unbeaten, which takes them up to sixth for now.
They also ended Leganes’ three-game unbeaten run, leaving Los Pepineros three points above the relegation zone.