Marcelino Garcia Toral's Villarreal appeared to have stolen three valuable points from the Ramon Sanchez Pizjuan when 20-year-old Luciano Vietto scored his third La Liga goal of the season in the 79th minute to round off a fine team move.
However, former Sevilla coach Marcelino – who complained post-match about his frosty reception – was left in despair come the full-time whistle as Denis Suarez squeezed in an 88th minute equaliser, before Unai Emery's side claimed the win in stoppage time.
Giovani dos Santos was caught napping in his own penalty area and tripped Benoit Tremoulinas as he attempted to clear his lines, allowing Carlos Bacca to stroke home the resulting spot-kick.
The win sees Sevilla move level on 22 points with Barcelona, their best ever haul in La Liga after nine games, while Atletico Madrid sit a further two points behind after a slender 1-0 win over Getafe.
The reigning champions made the short journey across Madrid and were rarely threatened by their neighbours, securing a victory to take full advantage of Barca's 3-1 defeat at Real Madrid on Saturday.
Mario Mandzukic scored an easy tap-in five minutes before half-time to give Atletico the lead, but the score should have been more one-sided as they wasted several chances in the first half.
And after beginning the second period brightly, Getafe gifted Atletico a numerical advantage when captain Alexis was sent off striking Mandzukic in the face.
To the credit of coach Cosmin Contra, Getafe attacked with desire in search of a late leveller despite being a man down, but Atletico's resolute backline held firm to seal all three points for the visitors.
The day's early clash saw in-form Malaga claim a third successive La Liga victory and move up to seventh thanks to a crushing 4-0 win over Rayo Vallecano.
Samu Garcia, Sergi Darder and Juanmi ensured Javi Gracia's men took a 3-0 lead into the break and Nordin Amrabat completed the rout from the penalty spot just after half-time.
Deportivo La Coruna held hosts Espanyol to a 0-0 draw at Cornella El-Prat in the day's only other game.
