Spain got what they deserved for the negativity in not playing Llorente.
Yes, and no, Barca had a bunch of games like that, while playing Messi as the central striker, but dropping deep a lot. Cesc maybe dropped too deep too often, but that's partly as they were rotating him and Silva frequently and, he made so many runs along the back four to go in behind after a pass and the passes never came. He scored from one of the first passes made as he made a run in behind and got a goal. His other two shots were both on target, one well blocked, one brilliantly saved.
Spains biggest issue was poor crossing, being too slow and indirect and ignoring that run in behind so so often, delaying the pass too long over and over again.
Had Llorente been playing, or pretty much any striker I couldn't see a huge change to the main problems, not passing in the guy up front.
Also as is sooo often the case, Cesc was their most direct, most deadly player on the pitch and they took him off and aside from generating some great laughs at Torres expense, did little afterwards. Never, ever take off the best player on the night when so many others are playing so badly.
I'll point out again, Alonso gave away the ball frequently, gave away stupid fouls(though not as many as normal), got caught on the ball more than I've seen happen to him, passed backwards SO often it was a joke and generally offered nothing defensively as per usual. No idea how he's in the team, Busquets wasn't exactly brilliant but, in that team there is no reason to play Alonso or two DM type players.
What they needed was to take off Alonso and put a striker on with Cesc or just ahead of him, that likely would have made the difference. While also, yes, Silva got the assist, he did 2 or 3 of those sideways passes in behind all night, great, except everything else he did was useless. He is such a tame shooter, no power, his really one cross that I can remember was straight at the keeper. Navas's time on the pitch was so much more effective overall.
Generally speaking Iniesta/Silva doesn't give you much width, very little good delivery, Silva is just weak and mostly lazy, Iniesta is actually good but ran with the ball so often, didn't pass early enough and ended up losing it. If he would pass a little earlier rather than go it alone he'd be so much more effective.