Total sales fell 0.1 percent month to month, held back largely by dropping automobile sales, although total sales were up 3.2 percent from September 2012.
Sales fell short of expectations. Economists had expected a 0.1 percent rise.
A drop in automobile sales of 2.2 percent led the decline. Sales rose 0.4 percent when data for automobiles is excluded from the total, the bureau said.
On a seasonally adjusted basis, total sales fell to $425.9 billion in the month.
The bureau said food and beverages sales rose 0.9 percent with grocery store sales up 1 percent. Sales at sporting goods stores rose 0.5 percent. General merchandise sales rose 0.4 percent.
Sales were flat at gas stations in September and down 0.5 percent at clothing stores, the bureau said.