The Yellow submarines had won the reverse fixture in Spain as Bayern hoped to overturn the deficit on Tuesday.
The Bavarians took the lead in the second-half courtesy of their mercurial finisher Robert Lewandowski to level matters on aggregate.
However, Villarreal levelled matter at the death through a clinical finish from Villarreal striker Samuel Chukwueze two minutes into stoppage time.
The Nigerian international’s strike was just about enough to help Villarreal progress into the semi-finals of Europe’s elite tournament at the expense of the Bundesliga Champions.
Following the shocking result for the Bavarians, Nigerians have taken to social media to heap praises on Super Eagles star Samuel Chukwueze after his wonderful goal for his Spanish side.
Here are some reactions from Twitter below: