The tie was all but over after the first leg as goals from Antoine Griezmann, Angel Correa and Kevin Gameiro handed Diego Simeone’s men a 3-0 aggregate lead.
And Eibar’s task was made even more difficult when Jose Gimenez headed home Nicolas Gaitan’s corner shortly after half-time.
However, a match that had produced little in terms of quality had a thrilling ending as Eibar - much to their credit - refused to cave in and two goals in seven minutes from Sergi Enrich and Pedro Leon saw the Basque club - who had reached the quarter-finals for the first time - take a 2-1 lead.
Atleti extinguished any slim hopes of what would have been a remarkable comeback, though, as Juanfran brilliantly lobbed Yoel in the Eibar goal with five minutes remaining to earn a draw and a 5-2 aggregate victory.
Simeone’s men consequently reach the last four for the first time since 2014, but he will perhaps be disappointed with his side’s failure to win having only drawn 2-2 at Athletic Bilbao in LaLiga on Sunday.
There was little to excite a half-empty stadium in a tepid opening, although the unmarked Fernando Torres perhaps should have done better when he headed wide from Gabi’s sixth-minute corner.
Correa also hit a well-struck left-footed volley that cleared the crossbar, while at the other end Bebe saw a tame 20-yard effort go wide of the left post for Eibar.
Josue Dorrio provided a rare bright note in the 26th minute with a stunning dipping volley that forced Atleti goalkeeper Miguel Angel Moya to fling himself to the left and make a brilliant one-handed save.
Eibar enjoyed a spell of possession towards the end of the half, but Atleti were comfortable in defence and Moya was troubled.
Any hope Eibar had of a rousing comeback was all but ended in the 49th minute when Gaitan’s superb outswinging corner from the left was emphatically headed home by Gimenez past a despairing Yoel.
Correa should have finished the job after springing the offside trap to latch onto substitute Yannick Ferreira Carrasco’s throughball, but he shot straight at Yoel’s legs when one-on-one.
Eibar pounced on that let-off in the 73rd minute. Leon saw a fierce strike cannon off the right post and Enrich was on hand to lash home the rebound.
It was 2-1 seven minutes later as Bebe’s whipped cross from the left was brilliantly guided into the bottom left-hand corner by Leon on the volley.
But, with five minutes remaining, Yoel was caught too far off his line and Juanfran lofted a superb volley over the stranded goalkeeper to salvage a draw for Atleti.