Team orders rule ties F1 in knots
It means the Spaniard, in a car that is now absolutely competitive after recent updates, has closed the gap on leader Lewis Hamilton and the prospect of a five-driver battle for the world title remains very much alive.
Of course, that point has become rather lost in the intense controversy about how Alonso secured the 23rd victory of his career.
The Spaniard was clearly handed first place on a plate by team-mate Felipe Massa on lap 49, the Brazilian slowing down out of the hairpin at Turn Six after his engineer Rob Smedley had told him on the radio: "Fernando is faster than you."
Ferrari have been fined $100,000 (£65,000) for a breach of article 39.1 of the F1 sporting regulations, which says: "Team orders which interfere with a race result are prohibited." The race stewards decided not to change the result but have referred the matter to the World Council of motorsport's governing body the FIA.
Ferrari claimed after the race that they had not ordered Massa to let Alonso past, which strictly speaking is true, even if the whole watching world understood the subtext of Smedley's message as clearly as the Brazilian did.
Let's be clear about this: Smedley's message was a clear, coded instruction to Massa to let Alonso through and this was therefore clearly an example of team orders.
But that is where the situation gets a bit murkier.
Just because Ferrari effectively asked Massa to let Alonso win, was that necessarily the wrong thing to do? Is it right that the F1 rules ban team orders? Did Ferrari even technically break the rule?
There are so many difficult areas here.
First of all, technically, Ferrari did not order Massa to let Alonso win, not in so many words.
Secondly, what does the rule actually mean? Did what Ferrari did interfere with the race result? How can anyone possibly know? They could, if they wanted, argue that Alonso, who had been significantly faster than Massa all weekend, was going to get past eventually. Or that they didn't want to risk a collision between their two drivers by letting them race.
They didn't do that. Instead, they have been forced into what many will view as the ridiculous charade of having to dress it up as Massa's decision.
Parallels will be drawn between this race and the notorious one in Austria in 2002, when then Ferrari boss (and now FIA president) Jean Todt ordered Rubens Barrichello to let Michael Schumacher past to win.
That day, despite repeated demands in the closing laps, Barrichello only ceded position on the run to the chequered flag. The resulting outcry - which started with Schumacher being booed on the podium and ended up with Ferrari being given a $1m fine - led to the rule banning team orders being introduced.
But I don't see it as the same situation. There was no need to deprive Barrichello of that win. Schumacher had dominated the start of the 2002 season and already had a significant championship lead at a race that came much earlier in the season than this one.
What happened in Hockenheim on Sunday was different. Alonso has been Ferrari's stronger driver all year and is clearly the only one who has a chance of the championship.
This - unlike the situation between the two Red Bull drivers at Silverstone - is not an example of two evenly matched drivers in one team battling it out for the title and the team making a call that potentially disadvantages one of them.
Massa has simply not been strong enough this season compared to Alonso for anyone to make a case that he will be consistently beating him for the rest of the season, and by extension feature in the world championship battle.
As BBC F1 analyst Martin Brundle put it during the race, Alonso has had a tough couple of weekends, suffering badly at the hands of some stewards' decisions, and he needs as many points as he can get to haul himself back into the title chase.
Schumacher himself was very interesting on this subject after the race on Sunday.
"Watching the TV occasionally (on the big screens during the race), I've seen Felipe being in first position and I felt happy because he is a good friend of mine," he said. "Then hearing that Alonso won the race I was wondering what kind of strategy was that?
"I have been criticised in the past for exactly that and I have to say that I would do exactly the same if I was in their situation. At the end of the day, what are we here for? It's fighting for a championship and there is only one that can win it.
"By the end of the year, if you think you would have lost the championship for exactly that point you will ask yourself, all the fans, the television, the journalists, why didn't you do so?
"If you go back to other years, other teams and other situations, in the last race there were clear team orders and everybody accepts those. Whether it's the last race, second last race or even earlier, what's the point?
"I can see that in the years when we did it, because we were leading so much, that people thought it was unnecessary and I can agree on that one in a way.
"But in principle I cannot. I agree with what's going on. You have to do it in a way that is nice and maybe not too obvious - make it nice fight. But there's only one target, and that's winning the championship."
It's worth pointing out that the previous version of this rule said "team orders that are against the interests of competition are forbidden".
Under that wording, you could even make the case that what Ferrari did was explicitly allowed, even encouraged, by the rules - in that letting Alonso win was absolutely in the interests of competition, ie in increasing the prospects of an interesting world championship fight.
That wording was changed because of its inherent vagueness, but there is a far wider point here - and that is whether the rule should be there in the first place.
Many people watching the German Grand Prix will doubtless have been disgusted by what happened, and feel that they were deprived of seeing two men battle it out to the finish.
But the reality of F1 is as David Coulthard described it after the race on Sunday: "Every team in this pit lane gives team orders and anyone who says they don't is lying."
F1 is a team sport; teams constantly manipulate races. Having a rule banning team orders doesn't mean they don't happen, it simply means teams have to find duplicitous ways of employing them.
Equally, I don't see the logic of an argument that says Ferrari should be penalised for this incident but teams and drivers should not have been punished for similar situations in the past.
The most obvious recent one that springs to mind decided the result of the world championship in 2007.
In the final race of the season in Brazil, Massa was leading then-Ferrari team-mate Kimi Raikkonen, with Alonso - then at McLaren - in third place and the Spaniard's team-mate Hamilton fighting his way back up the field, eventually finishing fifth.
Had Massa won, Hamilton would have been world champion - but Massa, clearly under instruction from Ferrari, gave up a victory in his home race so his team-mate could win the title.
No one complained then. So why now?