Double Formula One world champion Alonso seized the lead at the start, stayed in the hunt for the first third of the race and then fell off the pace as if driving through treacle after switching from soft to harder Pirelli tyres.
The Spaniard finished fifth in front of his home fans at the Circuit de Catalunya but was lapped by both the Red Bull and McLaren drivers.
"There is no denying that being lapped hurts," said Domenicali.
"It's even more painful after seeing a driver of Fernando's calibre putting on such a breathtaking display at the start and then fighting like a lion to keep drivers with clearly faster cars behind him for almost 20 laps."
Alonso was losing some three seconds a lap on the harder Pirellis, a fact that prompted Domenicali to observe wryly that at least nobody could accuse the Italian tyre company of favouring Ferrari.
The Spanish driver, who won with Renault in front of his home crowd in 2006, had performed brilliantly on Saturday to qualify fourth and sent a huge cheer up from the grandstands with his storming start past both Red Bulls.
As it turned out, it did not get any better than that.
"I tried to do the maximum, keeping the quickest ones behind me for around 20 laps, but after that there was nothing I could do," he said.
"We lack aerodynamic downforce. Here we did not have a wing that suited this track," added Alonso, whose car's new rear wing was ruled illegal by officials after Friday practice and had to be replaced.
"We must analyse carefully the behaviour of all the modifications we brought to this grand prix and understand why, in the space of two weeks, we have lost ground to Red Bull and McLaren."
Alonso's Brazilian team mate Felipe Massa suffered a gearbox problem and stopped by the side of the circuit, the team's first retirement of the season.
Ferrari remained third overall in the constructors' standings, with 75 points to leaders Red Bull's 185 after five races.
Alonso stayed fifth in the drivers' championship, a massive 67 points adrift of Red Bull's race winner and world champion Sebastian Vettel.
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