Kyle Allgood was the second confirmed death in the outbreak, which also killed an elderly Wisconsin woman.
"This confirms what we suspected for quite some time," said Ross Mason, a spokesman for the Idaho Department of Health and Welfare. "Confirming that, though, was important information and will help us in the future if we have similar situations."
The boy, who would have turned 3 in December, died Sept. 20 in Salt Lake City after developing a type of kidney failure caused by E. coli. Health officials had to wait for the results of genetic testing on the bacteria to determine whether his illness was from fresh spinach.
The test took time because the sample taken from the boy was fairly small, so technicians had to let it grow for several days at a laboratory before analyzing it, officials said.
The toddler became ill after having a fresh spinach smoothie, according to his mother, Robyn Allgood.
Last week, the FDA lifted a two-week consumer warning on fresh spinach. On Wednesday, the FBI searched two California produce companies for evidence of possible felony violations of federal environmental laws.
E. coli lives in the intestines of cattle and other animals and typically is linked to contamination by fecal material. It causes an estimated 73,000 infections each year in the United States, including 61 deaths, according to the federal Centers for Disease Control and Prevention.
Sources can include uncooked produce, raw milk, unpasteurized juice, contaminated water and meat, the agency said.