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Luis Enrique's team produced a largely laboured showing, but remain two points behind in-form leaders Real Madrid after Busquets blasted home inside a crowded penalty area deep into stoppage time.
Valencia would have been good value for a point at the Mestalla and almost led through Sofiane Feghouli and Alvaro Negredo before Busquets had the final word.
The match ended on an unsavoury note when Lionel Messi appeared to be struck by an object thrown from the crowd during Barcelona's goal celebrations.
Events off the field took a tragic turn ahead of the early kick-off between Atletico Madrid and Deportivo as clashes between rival fans left one dead and 11 injured.
Despite attempts from the LFP (National Professional Football League) to have the game postponed, Atletico won 2-0 thanks to goals from Saul and Arda Turan.
Sevilla remain three points shy of Atletico in fourth and were the day’s big winners as they romped to a 5-1 thumping of neighbours Granada.
Unai Emery's team put four matches without a win in all competitions behind them as Carlos Bacca opened the scoring when the visitors failed to clear Gerard Deulofeu's set-piece.
Youssef El Arabi's penalty ensured the match was level at half-time, but four goals in the last 25 minutes saw Sevilla run away with the contest.
Ever Banega converted the rebound after his volley came back off the crossbar, Bacca converted his second emphatically from close range and replacement Kevin Gameiro completed the scoring after crossing for Stephane Mbia to head home in the 89th minute.
Villarreal are three points and a place behind fifth-placed Valencia thanks to a 2-0 victory that meant 13 league matches without a win for basement boys Cordoba.
Lucas Vietto broke the deadlock midway through the first half and Ike Uche sealed the points after the interval.
