The Nigerian, 16, won weightlifting gold with a combined total of 196kg in the women's 53kg category.
The Commonwealth Games Federation says it will meet on Friday to determine her punishment following her positive 'B' sample test.
Amalaha was provisionally suspended from the Games after an 'A' sample was found to contain banned substances.
The samples contained amiloride and
hydrochlorothiazide, which are both prohibited as diuretics and masking agents.
After confirming the positive test, CGF chief executive Mike Hooper said: "I can't and won't speculate on what the outcome might be.
"We have a robust process in place that must be followed to ensure fairness to all."
Amalaha was the first athlete to fail a test at the Games, but Welsh 400m hurdler Rhys Williams and 800m runner Gareth Warburton both missed the competition after being charged with anti-doping rule violations.
Both athletes deny knowingly taking any banned substance.
The World Anti-Doping Agency recommends a standard two-year ban for a first doping offence.
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