Betis looked to be heading for their first league win in two months when Joan Verdu scored with 11 minutes remaining, but in the 91st minute Bueno struck for the second time in the game to earn Rayo their first draw of the season.
Antonio Amaya had given the hosts a first-half lead which was cancelled out by Bueno early in the second period.
Betis entered the game as the bottom club in the Primera Division, with Rayo just one place above them, but Paco Jemez's side move one point clear of the relegation zone thanks to the draw, while the Andalusians stay rooted to the bottom.
The hosts were able to welcome back Ruben Castro to the starting line-up for the first time this season following months out on the sidelines with a recurring back problem.
With their talisman back in the fold, Betis dominated the first half.
Jorge Molina came close to giving them the lead after 10 minutes but failed to get on the end of a cross from Alvaro Vadillo, and then centre-back Amaya netted the opening goal on 26 minutes, taking advantage of slack marking by Rayo's defence to head a corner from Nono into the net.
Castro nearly converted another corner from Nono a few minutes later but his shot shaved the post, and then Salva Sevilla missed the target twice in the space of a minute.
Molina was presented with a chance to double the lead shortly before the break when a through ball over the top by Sevilla played him in but the striker could only shoot straight at the legs of David Cobeno.
Rayo managed to produce a far better display in the second period, but first they had to endure a scare as Castro headed a cross from Vadillo off the crossbar on 50 minutes.
Rayo then went up the pitch and equalised. Jonathan Viera found space to shoot on goal and Betis stopper Guillermo Sara was unable to clear his effort properly, and Bueno gobbled up the loose ball to level.
The visitors grew in confidence and looked the likeliest team to find a winner, but Betis took the lead again thanks to an error from Cobeno and quick thinking from Verdu.
The goalkeeper rushed out to thwart the incoming Castro but could only push the ball out to the edge of the area and Verdu struck first time to send it into the top corner.
In the closing minutes of the game Castro was twice denied a goal that would have sealed the points and as time was running out Bueno made sure the former Rayo striker would rue his wastefulness.
Bueno raised his right foot to control a ball by Viera and then knocked it past Sara with his left to score his fourth goal of the season and earn a vital point for his side.