Thuong finished in last place in the women's floor exercise.
The two are the second and third confirmed cases of doping at the Beijing games, where the IOC is conducting a record 4,500 drug tests.
The first involved Spanish cyclist Maria Isobel who tested positive for the banned blood-booster EPO, from a sample taken before the Olympics started.
She was expelled from the games on Monday, although had apparently already left Beijing earlier of her own accord.
|The IOC is conducting a record number of tests at the Beijing games [EPA]
Kim, the first Beijing Olympian to be stripped of his medals, could now face a ban of up to two years from the international shooting federation.
Giselle Davies, spokeswoman for the IOC said Chinaese shooter Tan Zongliang would be promoted to take Kim's silver in the 50m event, with bronze now going to Russia's Vladimir Isakov.
Kim's bronze in the 10m competition would instead be awarded to American shooter Jason Turner.
Professor Arne Ljungqvist, head of the IOC's medical commission, was in no doubt that Kim had deliberately taken drugs.
"I feel the figures are rather encouraging"
Professor Arne Ljungqvist, head of IOC medical commission
"This beta-blocking agent is banned only in certain sports such as shooting and archery which require great control. Therefore I can only describe it, (the drug-taking) as deliberate."
He was more charitable when it came to the case of Thuong, whom he believed had been poorly advised.
"This was probably a result of poor information to a young athlete who was not sure what she could take."
The last summer Olympics in Athens in 2004 saw a record 26 doping cases, and with an increase in testing for the Beijing games the IOC had expected to see even more positives.
But with only three positives so far, approaching the half way point in the games, Ljungqvist said he was optimistic that deterrent methods may be paying off.
"My interpretation is that this a feature of increased awareness in the sports world that doping is unacceptable and you don't compete in the Olympic games if you are doped," he said.
"I feel the figures are rather encouraging."