The Uruguay striker robbed defender Francisco Noguerol in the 26th minute and after sprinting clear lashed a powerful shot into the bottom corner past goalkeeper Yoel Rodriguez.
Celta, relegated at the end of the 2006/07 season and 17th out of 22 in the second-tier standings, battled valiantly in front of their vociferous fans and almost snatched an equaliser in the 84th minute.
The impressive Roberto Trashorras cut in from the left and Jose Luis Mato headed the midfielder's cross against the bar.
Atletico will play Racing Santander in next month's two-legged semi-finals after the Cantabrians won 3-0 at Osasuna on Wednesday for a 5-1 aggregate victory.
Defender Ruben Gonzalez fluffed a golden chance to double the visitors' lead five minutes after the break, heading over from close range.
