Former Boca Juniors forward Sony Norde converted a free-kick in the 23rd minute to dash Mohun Bagan's hopes even as they struggled to convert their chances up front without Odafa Okolie.
With two wins, Dhanmondi who defeated United Sikkim in the previous outing finished second with six points behind group toppers Mohammedan Sporting (7).
As per revised schedule, the back-to-back semis will be held on Tuesday, the third place play-off on Wednesday before the summit clash on Saturday.
Mohun Bagan needed a draw to advance into the semis but CS Sabeeth was not fed with balls in the attacking third.
Norde's curling free-kick kissed the far post before finding the back of the net as Mohun Bagan goalkeeper Shilton Paul was clueless.
Dhanmondi kept on attacking while Mohun Bagan coach Karim Bencherifa tried to bolster the attack bringing in Shankar Oraon and Souvik Chakraborty.
But there was no danger to the visitors as Mohun Bagan looked a disjointed side with mispasses galore.
In their last tournament, Mohun Bagan were knocked out of the Federation Cup going down to Churchill Brothers in the semi-final.
They would now shift focus to I-League where also their chances are all but over as they are currently in sixth place in the 13-team table.
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