The Spaniard put his spot-kick over the bar to give Derby a dramatic 4-3 penalty shoot-out victory after the Saints had levelled the tie with a 3-2 win at Pride Park.
Leon Best also missed for Southampton in the shoot-out as the Derby players kept their nerve when it mattered in torrential rain.
The defeat was harsh on the visitors who recovered from conceding an early goal to come back and win the second leg with a goal from another ex-Derby player Grzegorz Rasiak.
Southampton started the night trailing 2-1 from Saturday's first leg and Derby got the best possible start when Darren Moore headed a corner from Matty Oakley inside the left-hand post.
But Southampton's reply was instant as Jhon Viafara volleyed into an empty net from 25 yards after Stephen Bywater could only head clear following a mistake by Moore.
There were no more clear chances in a frantic first half, but it was advantage Southampton in the 54th minute when Viafara took a pass from Best and drove a right-foot shot into the roof of the net from 12 yards.
Derby responded with a low cross from Stephen Pearson which Craig Fagan drove against the post, but Derby levelled on the night and regained the lead when Giles Barnes flicked on a corner and Best could only turn the ball into his own net as he tried to clear.
Former Derby manager George Burley made two telling substitutions when he brought on Djamel Belmadi and Rasiak, and both players combined to give the semi-final another twist.
Belmadi cut through Derby's defence on the left and then pulled the ball back before Rasiak turned to drive a left-foot shot in from 12 yards.
Rudi Skacel fired over in stoppage time and both sides had chances in extra-time before the penalty shoot-out which takes Derby through to the final where they will play either West Brom or Wolves.