Hamilton made an early switch to the hards on Lap 25 in a bid to undercut Carlos Sainz.
The Ferraris stayed out as they looked to extend their first stint to complete a comfortable one-stop strategy.
Shortly after the Ferrari pit stops, the race was halted after Kevin Magnussen’s heavy shunt, resulting in a red flag.
The red flag gave all teams the chance to change tyres, with Mercedes putting mediums on Hamilton’s car for the restart.
Horner felt without the mid-race stoppage, the two Ferraris would have beaten Hamilton.
“They had a bit of a stroke of luck because they went in very early for a one-stop strategy,” Horner told Viaplay. “I think in the end they would have been beaten by the Ferraris.
“But it is true that they had good speed and did well in terms of tyre wear, as we have seen from them all year.”
“It completely neutralised our race,” he added.
“But the good thing at that moment was that Charles switched to the hard tyre just like us. We were afraid that he would go for the medium compound.”