Ryoma Watanabe got an early opening goal for Urawa Reds, who were backed by a noisy contingent of their supporters at Lumen Field in Seattle.
But captain Lautaro Martinez had got Inter's equaliser in their 1-1 draw with Monterrey of Mexico in their first match at the tournament, and he repeated the trick to level matters here with 12 minutes to go.
Carboni, the 20-year-old Argentine who had not made an appearance for Inter in more than two years, then appeared in the 92nd minute to give the Italians the victory.
The result leaves Cristian Chivu's team in a good position to now go and qualify for the last 16, while a second defeat in as many matches means Urawa Reds are eliminated.
Winners of the Asian Champions League in 2023, Urawa Reds were aiming to bounce back from a 3-1 loss against River Plate in their opening game and they went in front in the 11th minute.
Takuro Kaneko made the goal with a good run down the right before his low cross was swept home first-time by Watanabe.
Martinez hit the crossbar from a header for Inter soon after, and it looked as if the UEFA Champions League runners-up might slip to a shock defeat when Henrikh Mkhitaryan missed the target from a good position in the second half.
But they got the leveller in the 78th minute when a Nicolo Barella corner from the left was deftly turned in by Martinez, who scored with an overhead kick as he fell back the way.
The stage was then set for Carboni, who had not played a competitive game since early October after suffering a serious knee injury while on loan at Marseille.
He was on hand to sidefoot into the net after a Petar Sucic shot hit teammate Francesco Esposito and ball broke to Carboni inside the area.
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