Alli, whose last competitive appearance came nearly 750 days ago for Besiktas, was brought on in the 81st minute for Como midfielder and goalscorer Lucas Da Cunha.
But it wasn't long before the former Tottenham man's debut turned into a night to forget.
Alli attempted to dispossess Milan midfielder and former England teammate Ruben Loftus-Cheek but only managed to step on the back of his rival's calf as the referee brandished a yellow card.
However, the referee was told to review the incident on the pitchside monitor and it wasn't long before he returned to the pitch to overturn the decision.
Despite the desperate pleas of Alli's Como teammates and Milan's Kyle Walker, who played alongside the midfielder at Tottenham, the referee was unmoved and sent him off in the 91st minute.
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Alli's red card had no impact on the result, as Da Cunha's opener was cancelled out by Christian Pulisic before Tijjani Reijnders netted the winner in the 75th minute.
The defeat was Como's 14th in the league and left them sitting in 13th, six points clear of the relegation zone.
As for Milan, they are seventh on 47 points.
Alli's debut came almost two weeks after he was named on Como's bench for the first time in what was his biggest step towards a return, although he did not enter the contest in what was a 2-1 loss to Roma.
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The former Tottenham and Everton midfielder was once again an unused substitute for Como's next Serie A clash, this time a 1-1 draw with Venezia.
Alli began training with Cesc Fabregas' side over Christmas, although the Spanish great was reluctant to claim whether it would lead to anything.
"Let's see. It would be to help him get in shape and nothing more," Fabregas said at the time.
But Fabregas elected to sign Alli on a permanent basis as the 37-cap England international penned a deal until 2026, with the option of a further 12 months.
"The club believes in Dele's potential and is committed to helping him find his best form," Fabregas said upon signing Alli.
"His experience and leadership qualities will certainly be useful to the team."
Alli's return to football, even if it ended in devastation, is the latest chapter in a rollercoaster few years for the midfielder.
In a highly-emotional interview with Gary Neville in 2023, Alli revealed he contemplated retiring at age 24 and even spent time in a rehab facility to improve his mental health.
Alli also revealed he was sexually assaulted at the age of six and began dealing drugs at the age of eight before he was adopted at the age of 12.
He also said he became addicted to sleeping tablets in an effort to quell his mental trauma and worries the problem is more widespread in football.
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