Horner said it was "unfair" to boo Vettel, who has suffered repeated ill-treatment this year and was again subjected to loud chants and heckles after winning Sunday's Singapore Grand Prix. (Agencies)
The 26-year-old star did his best to shrug off the jeers but Horner said the booing, blamed on a particular group of fans, might be getting under his skin.
"There is a small collective group and it is like a pantomime, but it is so unfair because it is not sporting," said Horner.
"The boy today has driven an unbelievable race. What you have witnessed today is one of the best drives that I have seen him produce in terms of raw pace, and I just don't think it is sporting to see a driver who has put a performance in like that not get the reception he deserves,” he said.
"He is a great kid. He has a great sense of humour. He has a big heart at the end of the day," he added.
Booing erupted after Vettel's wins in Belgium and Italy, and surprisingly at the less partisan circuit of Singapore, as Vettel moved closer to a fourth straight world title.
The opprobrium has been put down to plain boredom from fans, as the German has won more than half the races this season and already has one hand on the championship trophy.
On Sunday night, he led from pole position to the chequered flag in an astounding, if not terribly viewer-friendly, demonstration of uncatchable front-running.
But there is also residual anger after Vettel controversially ignored team orders and passed team-mate Mark Webber to win the Malaysian Grand Prix in March.
While Vettel apologised to Webber at the time, he later struck a defiant tone and insisted he would do the same again. Webber has announced his departure from the team at the end of the season.
Horner said it was "unfair" to boo Vettel, who has suffered repeated ill-treatment this year and was again subjected to loud chants and heckles after winning Sunday's Singapore Grand Prix.