Cristian Rodriguez struck deep into stoppage time to continue Atletico Madrid's remarkable European run of 14 consecutive victories as they eventually saw off a brave challenge from Viktoria Plzen.
The Czech side had successfully stifled last season's winners throughout and could even have gone ahead themselves when Vaclav Prochazka's brilliant free-kick forced Sergio Asenjo into a fabulous save just before the hour mark.
However, Atletico continued to probe until the final whistle and finally got their reward when Rodriguez received the ball on the edge of the area and gave Matus Kozacik no chance with a sweetly-struck volley - his first goal for the club since joining from Porto.
Atletico coach Diego Simeone had showed that his sights were firmly set on Sunday's Primera Division clash with Malaga as he made nine changes from the side that won at Espanyol at the weekend - and that set the tone for a subdued performance in front of a sparse crowd at the Vicente Calderon.
Indeed the holders could have been behind early on as Asenjo was generously awarded a free-kick after appearing to lose control of the ball in clearing after collecting a routine cross.
But the hosts soon began to dominate possession without overly threatening the Plzen goal as Emre Belozoglu and Rodriguez saw efforts fly off target whilst Adrian Lopez had a half-hearted appeal for a penalty waved away.
The visitors then had two decent sights of goal as Marek Bakos headed just wide when well positioned inside the area before Marek Hanousek tried to square for Bakos when shooting himself would have been the better option after robbing Emre five yards from his own goal.
Plzen went desperately close to the opener again just after the break as Asenjo produced a brilliant flying save to turn away Prochazka's ferocious free-kick, but the introduction of Raul Garcia seemed to give Atletico an extra impetus as they piled on the pressure in the final 20 minutes.
Garcia just could not get a good enough connection to Adrian's cross two minutes from time and Plzen seemed destined to leave the Spanish capital with a point when Kozacik produced his first serious save of the night to again deny the former Osasuna midfielder with a header from close range.
However, there was one final twist as, in the final attack of the match, a free-kick on the left was played short for Rodriguez who took a touch before volleying superbly into the far corner of the net to move Atletico to within touching distance of the last 32.