Uranchimeg claimed a 23-22 victory against the 28-year-old Stalker over an action packed nine minutes between the top two fighters in the world rankings.
The 30-year-old Mongolian, competing in his third Olympics, was energetic and clinical over the three rounds and perhaps should have won by a bigger margin, as he picked off Stalker with a number of clean rights in the third as the Briton tired.
The quarter-final victory brought a chorus of boos in the ExCel arena from the home crowd, who were quiet throughout the contest and were out cheered by a pocket of Mongolian fans.
"My soul is full of emotion. I have been in the Olympics three times now - Athens, Beijing and now London. It has been my long-standing dream to get a medal, which I have now achieved," Uranchimeg said after guaranteeing a bronze.
The narrow defeat was too much to take for Stalker, who threw his towel over his head and stormed out of the arena.
The British boxing captain appealed against the decision to world governing body AIBA but it was rejected.
"Yeah (he's inconsolable), he's not even speaking at the moment," Stalker's corner Dave Alloway said.
"To be one bout away and lose by one point, to lose it by such a close decision is the bit he's finding hard to believe.
It's one punch, one shot, one scoring blow," he added.
"He's devastated because he obviously wanted to get himself a medal at his home-based Olympics but it wasn't to be."
Ukrainian light-welterweight Denys Berinchyk, sporting one of the oddest haircuts in the boxing tournament, was dancing a jig in the ring after the second seed beat Australian Jeffrey Horn to set up a clash with Uranchimeg.
"It's going to be harder to fight with the Mongolian (than Stalker), but we will see," Berinchyk said before discussing the eye-catching mostly shaved style with a lengthy piece of hair left on top.
"The hairstyle is a traditional Ukrainian hairstyle called chub, and it was traditionally worn by Kazaki people from the south of Ukraine, who are known as good fighters."
There was a rare Cuban failure on Wednesday as light-heavyweight Julio La Cruz Peraza followed Stalker out of the Games when the top seed in the division was beaten 18-15 by Brazilian Yamaguchi Falcao Florentino.
Peraza was the more aggressive throughout the fight but Falcao boxed cleverly on the counter and picked off the Cuban as he came in to deservedly take the bout.
It was a second medal of the Games for the Falcao family after Yamaguchi's brother Esquiva was also guaranteed a bronze by reaching the semi-finals of the middleweights.
"I can't wait to see him and I will give him a hug and a kiss, and tell him that the Falcao brothers are victorious," the beaming light-heavyweight said after hugging and kissing members of the Brazilian media, as members of his team celebrated noisily nearby.
In the light-flyweights, top seed and defending champion Zou Shiming of China came through a tough bout with Kazak Birzhan Zhakypov to reach the last four and secure a bronze.
Zou's awkward style, throwing considered punches from different angles was enough to sway the judges into giving him a 13-10 win despite his attempts to hold on at the end as he took a number of blows in the final 30 seconds.
The victory set up a semi-final clash with Ireland's Paddy Barnes, who Zou thrashed in the last four en route to his gold in Beijing.
Barnes was unhappy with the scoring four years ago and his display in ousting lively Indian Devendro Laishram 23-18 suggested he should prove more of a match for Zou this time.
"Bronze medals are for losers. I'm fighting a guy in the next fight who beat me 15-0 in Beijing, my plan for the next fight is just to go out and score a point," Barnes said.
"I don't care if he beats me 15-1, just so long as I get that point, that's my Olympic gold. I'll go home a happy man."
The night ended on a sour note after Algeria's Abdelhafid Benchabla, the second seed in the light heavyweights, lost to Ukraine's Oleksandr Gvozdyk and a man in an Algerian shirt threw what appeared to be a table lamp from the media tribunes towards the ring long after the fighters had left the arena.
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