Horner dismissed the race as "quite peculiar" after Vettel, starting from sixth, battled through the chaotic, rain-hit grand prix before being hit by a puncture in the dying laps, leaving him out of the points.
Fernando Alonso was the surprise winner in Ferrari's clunky F2012, with Sergio Perez finishing a career-high second for Sauber, the team's best result since reverting to the ownership of founder Peter Sauber in 2009.
Horner said it was hard to draw conclusions from the race, which left Vettel sixth in the overall standings after the first two rounds. Team-mate Mark Webber finished fourth on Sunday and lies fourth overall.
"Looking at today's performance, one would have to say that Sergio Perez is currently the top favourite," Horner told reporters.
"Today was quite peculiar because if you look at it Sergio Perez was the quickest car on track. He was catching a Ferrari... and pulling away from a McLaren.
"It's difficult to draw too much out of the first couple of races... We know we have got things that we can improve on, and that's what we'll be focused on for China. But it's fairly unpredictable at the moment."
He said the strategy to bring Webber in for an early pit stop ahead of the field had been right, but Webber was unlucky as many others followed him, causing him to get stuck in the pit lane.
Meanwhile, Vettel's car faced multiple problems, including when the onboard radio broke and the team lost communications with him around lap 20.
Later, Vettel's left back tyre punctured and damaged the braking system, prompting frantic - and unheard - radio calls for the German to stop racing for safety reasons. However, Vettel brought the car home unscathed.
"We tried and tried on the radio but obviously he wasn't picking up on the radio. Thankfully the car did get to the end without the left rear brake failing," Horner said.
"That (puncture) was frustrating for Sebastian because for sure at least a fourth-place finish was on for him today."
Horner added that Ferrari and Sauber's performances were unexpected but he congratulated both teams, saying Perez especially drove a "great race".
"I think the only good thing is that the fans are in for a good year. The pace has moved around an awful lot," he said. "I think consistency will be important all the way through," he added.