The volume of retail trade fell 0.6 percent on the month after a revised 0.5 percent rise in August, the EU's statistics office Eurostat said. Analysts polled by Reuters expected only a 0.4 percent decline.
Sales of both food and non-food products fell and the volume of sales of automotive fuels was flat on the month.
Compared with the same period last year, September retail sales were up 0.3 percent, following three straight months of declines, the data showed.
The decline in retail sales was especially significant in southern Europe, with Portugal recording an all-time low with a 6.2 percent slump on that month and Spain's 2.5 percent decline was the biggest since April 2012.
Slovenia, now at risk of needing international financial assistance in case it fails to fix its banks and reform the economy, saw a 4.0 percent fall month-on-month in sales in September, the biggest decline since February 2009.
The European Commission expects economic recovery to get on a slightly more solid footing next year, but domestic demand is still weak as more than 19 million people in the Euro zone are out of jobs.
Weak consumer spending is also a concern for the European Central Bank which is expected to keep interest rates at record lows on Thursday despite a sharp drop in inflation, which fell to a nearly four-year lows in October.
