Super Eagles of Nigeria forward Samuel Chukwueze grabbed the headlines as Villarreal qualified for the semifinals of the UEFA Champions League.
The Yellow Submarine came into the second leg with a 1-0 advantage recorded at home.
The first half was tightly contested as both teams had chances of the counter attack.
Bayern Munich would go in front as in the 52nd minute when Robert Lewandowski converted a ball through to him by Thomas Muller.
Villarreal were behind with six minutes to go and manager Unai Emery made an attacking change by bringing in Chukwueze in place midfielder Francis Coquelin in the 84th minute.
The game seemed destined for extra-time, but a swift counter attack by Villarreal led to Chukwueze converting a ball through to him by Gerard Moreno at the near post past Manuel Neuer in the 88th minute.
With another goal, Villarreal defended well as they held on for the draw to knock out Bayern Munich one of the favourites for the title,