Horner was left trying to extract the positives from a weekend in which Red Bull undoubtedly had the best car, only to suffer pain in Spain over the course of the European Grand Prix event.
On Saturday it was Mark Webber who was put through the wringer, qualifying a wretched 19th due to brakes and hydraulics issues that had afflicted his car in final practice.
Then in the race itself, as Horner concedes, Vettel "was in a class of his own", leading by 20 seconds when a safety car came into play.
That was managed well enough by the team, but within two laps of it returning, Vettel's car incurred its first mechanical failure for 29 races as the alternator in the Renault engine gave way.
"We were in a commanding position, so it was very disappointing to have a DNF (did not finish)," said Horner.
"Together with Renault I'm sure we'll learn from it and hopefully we will not see a repeat.
"The comfort we must take out of Seb's performance was that he was in complete control and had tremendous pace.
"We know we have a quick car, and we have had three poles from the last three races, and that is encouraging."
With Vettel not scoring and Alonso going on to claim an emotional victory, the 24-year-old German is now 26 points adrift of the Spaniard in the championship.
In such a closely-knit title race, it underlined just how costly one DNF can be, but Horner knows that given the law of averages, Alonso will have his problems somewhere down the line.
"Fernando has done a tremendous job, scoring in every single race, but statistics say he has to have one bad weekend in 20," added Horner.
"It will hopefully balance itself out over the course of the season.
"Others had difficult days as well - Lewis (Hamilton) did not finish - but we have extended our lead in the constructors' championship by a further eight points.
"It was a positive weekend on the whole despite not achieving the maximum points we deserved."
Horner also exonerated Vettel his fit of pique, with the German tossing his steering wheel out of the cockpit within moments of his car grinding to a halt.
Horner said: "He had just retired from a commanding lead in a grand prix, but he waved to the crowd on the way back.
"He then came over to the pit wall to reassure everybody we have a quick car, and I think he took solace in his performance.
"He did everything right, the car was running very quickly. What happened was one of those things."