Vettel, 25, became the youngest triple champion in history this year. He also joined Juan Manuel Fangio and Michael Schumacher as the only F1 drivers to clinch three titles in a row.
Horner admits it will be hard to match the records set by seven-time champion Schumacher, but he is sure Vettel is yet to reach his peak despite the success the German has already enjoyed.
"It's difficult to see any driver beating 91 wins and seven championships," Horner said.
"Sebastian is 25, has three world championships, 26 wins from 101 starts, more than 40 podiums, 34 poles; he's had a remarkable career so far.
"As a driver he will continue to develop, to get better. We are yet to see the best of him.
"F1 today is different to 15 years ago. There's a much more level playing field in terms of everyone having the same tyres, the same amount of testing, limited engines.
"Only time will tell what Sebastian is capable of in the future but the exciting thing is we are yet to see the best of him."
Horner conceded Red Bull will need to take another step forward in 2013 if it is to stay ahead of its rivals after what the team boss labelled one of its toughest seasons to date.
"We will apply the lessons we have learned in each of the last three years, [as well as] the lessons we've learned this year, and look to apply them for next year," he added.
"We're up against some formidable opponents, they won't be sleeping over the winter and we will have to improve. We have to further the car and the team in order to maintain the kind of performances we've achieved not just this year but over the last three years.
"It gets harder, never easier. This year for sure was the hardest of the three. I think we had to show true strength of character as a team to fight our way back into the drivers' and constructors' championship.
"We have a great foundation, a great basis. Even if we took this car to the first race next year, it would be a good starting point. But Formula 1 doesn't stand still and we have to evolve, we have to improve.
"Everybody in the team knows that. We have improved over the last three years and we'll be looking to do the same next year."