The consensus forecast called for the rate to hold at 12 percent. Instead, it hit a record high in the eurozone, the 17 countries that share the euro as currency.
In the broader 28-member European Union, unemployment held steady at 11 percent with rates above 10 percent in 12 countries in the EU and unemployment rates for youth above 20 percent in 15 countries.
Unemployment held at 26.6 percent in Spain and was last listed at 27.6 percent in Greece, where the latest figures available are from July.
In Europe's largest economy, Germany, the unemployment rate dropped slightly from August to September, reaching 5.2 percent from 5.3 percent. In France, the second largest economy in the region, unemployment ticked higher, rising from 11 percent to 11.1 percent.
Italy's unemployment rate rose from 12.4 percent to 12.5 percent. In Poland, it held at 10.4 percent. In Portugal it fell from 16.5 percent to 16.3 percent.
The unemployment rate in Britain was not included in the report. The last entry, from July, was 7.6 percent.
Eurostat said unemployment in the EU reached 26.8 million men and women, 19.4 million of those living in the eurozone. Unemployment month to month rose by 61,000 in the EU and by 60,000 in the eurozone, the data agency said.