The prodigious attacker earned the the Spanish side passage to the round of 16 at the expense of the Russian outfit
Marcelo Bielsa's men entered the clash needing a least a 1-0 victory to progress after a 2-1 first-leg defeat in Moscow, and amidst a tight contest, the young Spaniard went on to seal victory for his side when he struck from an Inigo Perez corner kick.
Despite the hosts needing a goal to go through, it was the Russian side who looked most likely to score early on. Felipe Caicedo forced Gorka Iraizoz into his first save of the match only minutes after the opening whistle with a drive from the edge of the box.
Lokomotiv started much more positively, but the home side were soon able to settle into the match. The fans at San Mames watched their side attempt to implement their fluid attacking football.
However, neither goals nor goalmouth opportunities appeared in the first half. Each time an attacker worked his way into the box, there would always be a diving body or stray foot to block every effort. As a result, the two sides cancelled each other out and Caicedo's opening strike was the only effort fans witnessed in the first 45 minutes.
After a dominant start to the second half, Los Leones finally appeared to be gaining the advantage, but Fernando Amorebieta dampened his side's hopes when he was sent off after bringing down Roman Shiskin to earn his second yellow card and subsequently see red.
Losing a man did not faze Athletic, however, but instead inspired them. The Basque side finally broke the deadlock when Perez's corner was flicked on by Llorente to the far post where Muniain slotted past Guilherme to give his side the goal that they needed to progress to the next round.
The rest of the match was a tense affair as the Moscow side looked to pressure their opponents into conceding, while Bilbao almost doubled their advantage on several counterattacks, but in the end, the home side held on for the victory.
With the win, Athletic progress to the round of 16 and will face the winner of the tie between Manchester United and Ajax.