Inter led by two goals from the impressive Ivan Perisic and Stevan Jovetic, before what was supposed to be a routine backpass from substitute Kondogbia looped over his own goalkeeper and nestled into the top corner from fully 40 yards, stunning the crowd of over 32,000.
Inter goalkeeper Daniele Padelli, who had no chance and held out his hands in astonishment, shrugged off the embarrassing mishap, saying afterwards it was merely “unlucky”.
Chelsea boss Antonio Conte was sympathetic: “It can happen, can happen — this is football.”
But the French midfielder Kondogbia was soon trending on Twitter with many calling his unintentional long-distance lob the best own goal of all time.
It overshadowed what had otherwise been an impressive performance by Inter, and in particular Manchester United target Perisic.
The Croatian winger played a central role and scored the Serie A side’s second goal in the 53rd minute, latching on to a pass from Jovetic before applying a smart finish.
In contrast, Chelsea’s big-money signing Alvaro Morata was quiet on his first start since moving from Real Madrid last week and made little impact before being substituted in the 64th minute.
Conte said that Morata, captured in a deal reported to be worth up to 80 million euros ($94 million), was “working well” but conceded he needed to do better.
“Today he tried to do his best, for sure, but he has to improve,” said Conte.
Inter dominated the early stages. In the first few minutes a defence-splitting Milan Skriniar pass found Antonio Candreva — reportedly a Chelsea transfer target — who forced Chelsea goalkeeper Thibaut Courtois into a fingertip save.
With the game going a bit flat, the English champions grew into their own. Willian had Chelsea’s first real chance with a deflected effort in the 27th minute, before David Luiz fizzed a freekick over.
Inter found the breakthrough in the third minute of first-half stoppage time when Jovetic was awarded a penalty after being fouled in the box. His first effort was saved but the striker slotted home the rebound.
After Perisic’s second, Inter nearly made it 3-0 as he squared to substitute Joao Mario, only for the midfielder to shoot straight at Courtois.
Kondogbia’s unfortunate intervention set up a nervy finish but Chelsea were unable to force the leveller.
It was a second defeat on the spin after losing 3-2 to Bayern Munich in Singapore.