Plzen needed a first win on Italian soil in 12 years to keep their European campaign alive, and they almost made a spectacular start when Pavel Sulc flicked the ball on to Lukas Kalvach, whose powerful volley from just inside the area forced a flying save from Ivan Provedel after five minutes.
Provedel so nearly became the villain for his side just seven minutes on, passing the ball straight to Matej Vydra, whose shot clipped the top of the crossbar.
Le Aquile finally put the visitors under real pressure midway through the half as a neat turn and shot from Pedro had Martin Jedlicka at full stretch to turn it round the post, before the goalkeeper had to make sure Nuno Tavares’ low drive was flashing just wide.
No big opportunities for the hosts meant they failed to score before the break for just the third time in nine matches, yet at least Provedel saving Lukas Cerv’s clean strike in the final seconds meant they went in level.
However, just seven minutes after the restart, Provedel was not able to preserve Lazio’s lead in the tie.
A sustained period of pressure from Plzen culminated in Rafiu Durosinmi knocking Kalvach’s cross down to Sulc, who powered home his fourth UEL goal of the season.
In response, Marco Baroni’s side were laying siege to the Plzen penalty area, but other than a tame Gustav Isaksen shot straight at Jedlicka, they were failing to create clear sights of goal.
That was until the final 15 minutes, when the man who broke the deadlock in the Czech Republic last week again turned the tie in Lazio’s favour.
Alessio Romagnoli rose highest to head Mattia Zaccagni’s corner against the base of the post and over the line before the goalkeeper could claw it away.
Miroslav Koubek’s team pressed for a goal that would take the tie to extra-time, but the chance did not come.
Plzen bow out having now won just twice on the road in their last 19 UEL matches, while Lazio move on to face Bodo/Glimt in the quarter-finals.
Flashscore Man of the Match: Alessio Romagnoli (Lazio)