Atletico, which won its home semifinal 4-0, finished with a 6-3 aggregate to reach its first Copa del Rey final since 2000, when it lost to Espanyol. The Madrid side last won the trophy in 1996.
Atletico will play Sevilla in the May final after the 2007 champion booked its place Wednesday by beating Getafe 2-1 on aggregate.
Santander opened the scoring in the third minute at Sardinero Stadium when a Sergio Canales corner rebounded into the net off the head of Atletico's Juan Valera.
Atletico conceded another own-goal five minutes later when Jose Moraton volleyed Jose Antonio Reyes’ free kick into his own net.
In an outstanding individual play, Atletico midfielder Jose Manuel Jurado juggled the ball over a defender, exchanged passes with striker Sergio Aguero and shot past oalkeeper Mario Fernandez in the 52nd.
Santander's Francisco “Xisco” Jimenez and Mohamed Tchite scored two late goals.
Santander was reduced to 10 men in the 70th minute when Christian Fernandez was sent off for elbowing Ibrahima Balde in the face.
Both sides played attacking football and worked to create scoring opportunities.
Aguero failed to strike the ball cleanly in the fourth minute when he was sent a pass in front by Valera.
Santander's Fernandez delivered a dangerous cross in the 13th that Gonzalo Colsa struck just wide.
Aguero came close again in the 41st when he rose to head a Reyes cross just side of the right-hand post.
Aguero and Reyes were replaced for the last half hour as Atletico coach Quique Sanchez Flores looked ahead to Sunday's league encounter with Barcelona.
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