Lionel Messi scored a second goal with a stoppage-time penalty to give Barcelona a 3-2 victory at Valencia on Saturday that was overshadowed by a serious knee injury to Andrés Iniesta.

Messi opened the scoring and had the last word when he beat Diego Alves with a well-taken penalty that slid just between the diving goalkeeper and the post.

The hotly contested game was marred both by Enzo Pérez’s tackle that forced Iniesta off on a stretcher and a fan throwing a water bottle at Barcelona’s players while they celebrated Messi’s winner. The bottle appeared to strike Neymar’s head and hit other Barcelona players when it was tossed into their huddle.

The win lifted the champions to the top of La Liga. Barcelona are one point ahead of Atlético Madrid and Real Madrid before they both play their matches, against Sevilla and Athletic Bilbao respectively, on Sunday.

After Pérez’s challenge in the 12th minute Iniesta clutched his right knee and called out for help. The Spain midfielder’s knee appeared to buckle from under him. He was clearly in pain and held a hand over his face when he was put on a stretcher and carried off. The club issued a report saying Iniesta had injured a ligament and part of his right knee. The 32-year-old will undergo further tests when he returns to Barcelona.

“The worst news is Iniesta’s injury,” Barcelona coach, Luis Enrique, said. “But the team showed the desire it has. How we won says a lot about the spirit and character of this team.”

Enrique was also furious that Pérez was not booked for the tackle on Iniesta.“It was a clear action in which we saw a player injured and yet there was no yellow card,” he said. “Tomorrow, we will see how bad the injury is, but yes, he will be out for weeks. It’s a serious injury.”

Valencia rallied to take the lead through goals by Munir El Haddadi and Rodrigo Moreno early in the second half before Luis Suárez scored to make it 2-2. Messi snatched the win from the penalty spot after he passed the ball to Suárez, who was fouled by Aymen Abdennour in the box.

Messi’s goals took his league-leading tally to eight. They were his fifth and sixth goals in three matches since recovering from a right groin strain that sidelined him for three weeks. He scored a hat-trick to lead a 4-0 victory over Manchester City on Wednesday in the Champions League.

Troubled Espanyol produced a stirring second-half comeback to draw 3-3 at home to Eibar and ease the pressure on Quique Sánchez Flores.

An own goal by Diego Reyes and simple tap-ins from Sergi Enrich and Kike García put the visiting side 3-0 up before half-time. Hernán Pérez put Espanyol back in contention in the 67th minute, while Pablo Piatti pulled another goal back.

Espanyol’s hard work at getting back into the game risked being undone when the striker Felipe Caicedo was sent off for a double booking but Léo Baptistão grabbed a point with a thumping low finish from outside the box in stoppage time.