The championship leader stretched his advantage to 34 points, with Jenson Button ending a dreadful run of form with a spirited drive to take second, gaining a place when Sebastian Vettel was punished for a late overtaking move on him.
Vettel's pass on Button in the penultimate lap, completed with all four wheels off the track, was investigated by the stewards and they punished the German with a 20-second penalty that dropped him from second to fifth.
The top three had been comfortably clear of Kimi Raikkonen, who was promoted to third, with the Sauber duo of Kamui Kobayashi and Sergio Perez impressing to score good points in fourth and sixth.
Michael Schumacher pitted late to slip behind the Saubers into seventh, while Alonso's nearest challenger in the championship, Mark Webber, struggled and had to settle for eighth.
Germans Nico Hulkenberg and Nico Rosberg rounded out the top 10.
It was an afternoon to forget, however, for Lewis Hamilton. The McLaren driver was celebrating his 100th Grand Prix start, but his race was effectively ended by a left rear puncture early on.
Hockenheim was a picture, with the rain of the previous two days having disappeared. The drivers had had limited running time in dry conditions, and there was a sense before the race that it could lead to an unpredictable race.
It did not begin that way, however, with Alonso pulling away superbly and the top drivers holding their places. Felipe Massa and Romain Grosjean, mired in the midfield, lost their nose cones and needed replacements, while Hamilton and Bruno Senna also made enforced early pit stops.
Button meanwhile progressed while his team-mate struggled, overtaking Hulkenberg and Schumacher with DRS-assisted manoeuvres to climb into the top three.
Raikkonen had shown pace in the first stint, but a decision to continue on a fresh set of soft tyres proved costly, as the three men ahead of him eased away on the more effective medium compound rubber.
Button, meanwhile, was afforded an unlikely lifeline by Hamilton. Having pitted while well off the pace, he found himself right in the thick of the contest between Alonso and Vettel. Much to Vettel's displeasure, the Brit unlapped himself, as he was within his rights to do, and fought to do the same against Alonso. That whittled down the gap between the top three, and when Button pitted a lap earlier than his rivals, he managed to overhaul Vettel and move up to second.
It looked as if he might be able to then take the fight to the Spaniard, but the double world champion was never troubled, and in the final few laps began to pull away to safety.
Vettel, meanwhile, got a late lease of life and harried Button for second place.
Halfway through the campaign, Alonso has now opened up a significant advantage in the championship standings, and overhauling a man who appears to be driving at the peak of his powers this season is starting to look like a very tricky proposition.