Lionel Messi converted a 94th-minute penalty in a bad-tempered match overshadowed by a serious knee injury to Iniesta.
Valencia's sporting director Jesus Garcia Pitarch railed against the "absolutely lamentable" display of the referee after Barcelona snatched a controversial 3-2 win at Mestalla on Saturday.
Lionel Messi converted a 94th-minute penalty in a bad-tempered match overshadowed by a serious knee injury to Barca's Andres Iniesta.
Valencia are likely to face action from La Liga authorities after Neymar was struck by a plastic bottle thrown from the crowd as the Barca players celebrated the winner.
However, Valencia were incensed that Barca's opener was allowed to stand despite claims for offside and the home side were angered further when referee Alberto Undiano Mallenco didn't send off Sergio Busquets before half time.
"When Undiano Mallenco and his assistants see this match again they ought to be ashamed of having played such a part in a game that Valencia didn't deserve to lose," Pitarch thundered to BeIN Sports Spain.
"It is lamentable, absolutely lamentable that refereeing decisions prevented Valencia from taking a point or more from this match."
Valencia coach Cesare Prandelli took charge of his first game at Mestalla and nearly oversaw a huge upset as goals from Barca loanee Munir El Haddadi and Rodrigo overturned a Messi opener.
"I don't like to talk about referees, but the images speak for themselves," said Prandelli.
Luis Suarez's equaliser set up a grandstand finish and Messi coolly slotted past Diego Alves from the spot after Suarez had been felled inside the area deep into stoppage time.