The surplus, listed as an initial estimate subject to change, is also a sharp gain over September 2011 when the eurozone posted a trade surplus of $2.1 billion.
The 27-member European Union posted a $16 billion deficit in September compared with a $13.8 billion deficit in September 2011.
From August to September, EU exports dropped by 1.5 percent while imports fell 1.7 percent, Eurostat said.
Exports from the EU to most major trading partners rose in January through August from the same period of 2011. The exception was India, which experienced a 5 percent decline in goods exported from the EU.
The largest gains in exports came in trades with Russia, South Korea and Japan where exports rose 18 percent, 18 percent and 17 percent, respectively.
Despite those gains in exports, the EU still runs a deficit in trades with Russia, and Japan, but each deficit has declined in the first eight months of 2012 from the same period of 2011.
The trade deficit with China also declined January through August of 2012 from the same period in 2011.