Zinedine Zidane continued with his rotation policy by changing half of his squad from the 3-1 loss at Real Sociedad last week, but his side produced another underwhelming display.
Following a first half that saw them rely on Keylor Navas to keep them level, Madrid fell behind after the hour to a Loren Moron strike and their former player Jese added a second 15 minutes from time.
In what was billed as a possible farewell for a number of players ahead of a period of rebuilding, the home players were heavily jeered as they closed out a season with another new low and Gareth Bale languished as an unused substitute.
The game had a scrappy feel to it and it took 28 minutes for the first serious shot to arrive, with Navas tipping Marc Bartra's curler over the crossbar.
Karim Benzema squandered Madrid's best opportunity of the first half as he picked out the post from 14 yards - the sixth time he has hit the woodwork this term.
And that miss almost proved instantly costly as a backpedalling Navas was forced to deal with Giovani Lo Celso's chip.
Betis were given a let off just before the hour mark when Vinicius Junior's shot was smothered by Pau Lopez at his near post, but it was the visitors who took the lead four minutes later through Moron.
Andres Guardado was given plenty of space down the left and picked out Moron at the back post for a first-time finish into the roof of the net, before Jese steered home a second after being teed up by Junior.
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If nothing else, Madrid had made the Bernabeu a tough place to visit since Zidane returned in March. They had collected 15 points from 15 on home soil under the Frenchman, compared to two points from a possible 15 on their travels during the same period.
They have flattered to deceive for too long, though, and this humbling defeat - leaving them with a lowly 68 points for the season - has set them back even further.
Navas will be missed
Zidane has refused to comment on speculation that Navas will be on his way out in the summer, but if this is to be his final game in a Madrid shirt then he did not let himself down. The Costa Rica international produced two good saves in the first half and a couple more in the second, only to be let down by his defence for Betis' two goals.
Bale the bystander
Bale is another one of those facing an uncertain future at the Bernabeu. He returned to the squad today after a two-game absence but Zidane's decision not to use him felt instructive. An instrumental part of Madrid's trophy-laden first spell under the Frenchman, it is clear that the Bale no longer has a part to play in the Spanish capital.
With this disappointing campaign now finally over, Madrid have a couple of months to strengthen their squad before reconvening for pre-season training. Betis, meanwhile, take on Major League Soccer side DC United in a post-season friendly at Audi Field next week.