Playing his first game back after a knee injury, Puyol landed heavily after leaping for the ball in the second half of Barca's 2-0 victory and his arm was left in a gruesome position.
He was taken to hospital overnight and tests have confirmed that the Barca captain will be missing for two months.
Puyol's injury means Barcelona coach Tito Vilanova faces another unwelcome defensive conundrum for Sunday's first Liga Clasico of the campaign at home to Real Madrid.
Puyol appeared in good spirits on Wednesday morning.
"Good day! The sun always comes out again... thanks for all your messages! A big hug," Puyol wrote on his Twitter feed, adding that he would be back to full fitness soon.
Barca will sorely miss Puyol's experience and inspirational do-or-die attitude on Sunday and if Gerard Pique does not recover from his own injury in time, Vilanova may again be forced to deploy new signing Alex Song alongside fellow converted midfielder Javier Mascherano.
Neither were convincing in Barca's 3-2 comeback win at Sevilla in La Liga at the weekend and Song has yet to settle properly after joining from Arsenal in the close season.
Vilanova also has the option of throwing youth academy graduates Marc Bartra or Andreu Fontas into the fray, although it would be a major gamble given the importance of the clash.
A win for Barca, who have won all six of their La Liga games and top the standings by two points from Atletico Madrid, would put them 11 points clear of their great rivals.
Jose Mourinho's side, who play at Ajax in Champions League Group D later on Wednesday, have already lost twice, the same number of defeats as in the whole of their La Liga-winning campaign last season.
"I have always said it, we have always had problems in central defence but we will get through it," Vilanova told a news conference after the Benfica match.
"It's not just a question of what Barca loses for the Clasico on Sunday but also what it loses in terms of all the other matches," he added.
Barca had been forced to "convert players into positions which are not theirs", he said, but could potentially count on "homegrown players, which is what we have them for".
Puyol's injury took some of the shine off yet another win for Vilanova's men, who have won all eight of their matches in La Liga and the Champions League.
Real did manage to get the better of them in the Spanish Super Cup, winning the second leg of the traditional season-opener at their Bernabeu stadium 2-1 to level the tie at 4-4 and take the trophy on the away goals rule.
There was better news on Tuesday for Vilanova on the fitness of Andres Iniesta, who returned from Spain duty last month with a muscle strain but came on in place of Cesc Fabregas for the final 20 minutes of Tuesday's game.
Forward David Villa, who is gradually coming back from a broken leg sustained in December and came off the bench to score the winner at Sevilla, replaced Pedro with around 10 minutes left and looks to be back to something close to his best.