
The draw puts Getafe into the final on a 4-2 aggregate result, since Santander lost the first leg 3-1 in Getafe three weeks ago.
Getafe will face either Barcelona or Valencia in the final.
Santander gave the capacity crowd hope by taking the lead after just seven minutes, when local hero Pedro Munitis scored with a left- foot drive after being set up by fellow veteran Jorge Lopez.
Munitis and Ebi Smolarek had good chances to score a second crucial goal for Santander. But the hosts' hopes started to evaporate in the 76th minute, when winger Oscar Serrano was sent off for a second yellow-card foul.
And just four minutes later, the tie was effectively over when the ageless Francisco Casquero shot home Getafe's vital away goal, on a pass from Juan Albin.
This left Santander with a mountain to climb, needing two more goals in just 10 minutes - and playing with 10 men.
"We fought hard to get into the final," Casquero told Cadena COPE at the end, after saying that he had scored "a very important goal."
"Now we hope that things will go better for us in this final than in last year's," Casquero said.
Last season Getafe reached the cup final for the first time ever, only to lose 1-0 to Sevilla.
Getafe are enjoying the best ever season in their modest history, as they are also in the quarter-finals of the UEFA Cup, where they will meet favourites Bayern Munich.
Getafe coach Michael Laudrup is one of the candidates to take over at troubled Barcelona from Frank Rijkaard, at the end of the season.
Rijkaard will be under even more pressure to leave if Barca lose away to Valencia on Thursday, in the other semi-final.
The first leg was a 1-1 draw in Barca's Camp Nou.
Barca will make the trip down to Valencia without injured stars Lionel Messi, Deco and Ronaldinho.