Mourinho, who was sacked by the Serie A club on Tuesday, criticised Smalling in November for being unable to manage his injuries after a five-month spell on the sidelines.
The 'Special One' told reporters the former Manchester United defender 'isn't capable of playing through pain'.
He went on to say that Smalling 'holds something back' before questioning the 34-year-old's pain threshold.
He also suggested that Smalling 'maybe struggles to sleep with toothache' - a notion that led to sections of the Roma fanbase, turning on the Englishman.
Following Mourinho's exit earlier this week, Smalling took to Instagram to have his say on the matter and defended himself against the accusations from the former Roma boss.
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"Since signing for AS Roma in 2019, my commitment and loyalty to the club has never wavered," Smalling wrote in a post Smalling shared in both English and Italian.
"The minute I stepped foot in Roma, I instantly felt at home. Roma is my home, and the relationship I have built with AS Roma fans is something I cherish dearly.
"For that reason I wanted to jump on here to address some of the rumours that I have seen circulating over recent months. Let me start by clarifying that I have never asked to, nor even contemplated, leaving this great club.
"Speaking openly, the last few months have proved to be some of the most frustrating of my career. There are things in this game and in life that we can control, and others we simply can't. This injury has been one thing that we couldn't.
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"No footballer wants to spend their days in a treatment room, and this period of time away from my teammates has challenged me, with setback after setback. I have, and will always, put the needs of my team-mates first, but the absolute priority for the medical team is to guarantee that I can play a significant role in the latter part of the season and for seasons to come."
Smalling is pushing for a return to action in the coming weeks after suffering patella tendon tear in early September.
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He revealed he has been receiving injections to help speed up his recovery and avoid having surgery.
The defender also explained how he has been following instructions given to him by the club's medical team rather than making his own decisions.
"Guided only by specialists, I have been open to all solutions, short and long, and any insinuation that I have dictated a treatment plan are false," Smalling continued.
"With surgery not an option proposed by any specialist I have engaged with, I have to trust the expertise that guides my recovery plan which, contrary to popular belief, does include painkillers. A lot of them, in fact.
"The absolute priority is guaranteeing I can play for AS Roma at the highest level for years to come. Your patience and loyalty as I work on getting back to my best is greatly appreciated. I look forward to seeing you all soon.
"Additionally, I would like to take this opportunity to thank Jose and his team for their support over the last three seasons and officially welcome Daniele [De Rossi, new Roma head coach] to the club. Forza Roma."