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Deepika crumbled at the crunch as An San won 6-0, clinching the first three sets.
Atanu Das will next meet Takaharu Furukawa of Japan on Saturday for a place in the quarterfinals of the individual competition.
The Indian number one had earlier seen off a tough challenge from Chinese Taipei's Deng Yu-Cheng in a five-setter to move into round two.
Debutant boxer Pooja Rani (75kg) won her easy opening bout without a fuss to enter the last-eight stage.
Following the early exit of Atanu Das, Pravin Jadhav and Tarundeep Rai also crashed out in the round-of-32 stage of the men's individual event in Tokyo 2020 in Tokyo on Wednesday.
Japanese tennis superstar Naomi Osaka dropped out of the Games after she was beaten in the third round.
Gomboeva quickly regained consciousness after collapsing but needed to be stretchered out of the arena by medical officers.
The world No.1 finished with 663 points, while 20-year-old Korean prodigy An San (680) topped the qualification round with an Olympic record score of 680.
The quartet of Deepika Kumari, Atanu Das, Tarundeep Rai and Pravin Jadhav entered the mega event with renewed hopes of winning the country's first Olympic medal in the sport.
The major absentee is Jofra Archer, who is still recuperating from an elbow injury. Chris Woakes is also out with a bruised heel.