No he didn't. The shot everybody tries to supposedly show of his insane chin against Justin literally hits his chest and the follow up barely clips him because he's turned his head away from it instead of leaving his chin out.
Nobody's getting KO'd here unless they're Goulet.
There's no particularly strong evidence Khabib had a great chin. He was good at / lucky to always barely get hit, or only get hit after his opponents had slowed and couldn't put out their full power. He never once took some Nelson/Lewis shot and walked through it.
More importantly though, it's very hard to get KO'd when you spend 90% of your fights on top of your opponent or having them tied up. Of course he's not getting KO'd as one of the most successful grapplers of all time. That was the entire intrigue of the Tony fight as Tony actually was effective at fighting off his back.