Button and Brawn team-mate Rubens Barrichello, who has now signed for Williams for next season, failed to score points on just three occasions between them.
In contrast, Red Bull duo Vettel and Mark Webber had a tally of 12 no-scores.
Horner admitted there was no room for complacency, and that he fully expected their rivals to be working as hard as ever in the close season.
But despite this, he said there were plenty of positives to be taken from the season.
"Second is a fantastic achievement for the team," stated Horner.
We will learn a lot of lessons from this year, which will only make us stronger going into 2010
Christian Horner
"In many respects the team is still very young and it's only our fifth season in Formula One.
"To have achieved 16 podiums, six wins, five pole positions and six fastest laps, including four one-two finishes, as well as in excess of 150 points, is a massive achievement.
"We were championship contenders right up until the penultimate race, however, the championship ultimately wasn't lost in Brazil.
"You have to show respect to the season Jenson and Brawn had, with a very dominant early display in the championship. We were playing catch-up thereafter.
"Although second is one place off our ultimate target, it's still a very good result," added Horner.
"We will learn a lot of lessons from this year, which will only make us stronger going into 2010."
Vettel, who is in Beijing for the Race of Champions, also believes Red Bull can build on their successful year.
"You can't change yesterday but you can change tomorrow," he said.
"It is necessary to look back and understand what we've done wrong and the fact is that five times this year we didn't finish.
"But it's not time to regret, it's time to learn lessons and then look forward to next year.
"There is only one step better we can do and there is no question that is the target."
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