A so-called flash estimate of the region's Composite Output Index, an advanced measure with 85 percent of the pertinent data available, came in at 45.9 in September compared with a revised 46.3 posting for August.
Under 50 in the index indicates a contraction and the further away from 50 the faster the contraction.
Above 50 indicates growth.
For service industries, the Purchasing Managers Index in September hit a 38-month low at 46, down from 47.2 in August, which was, as of a month earlier, a two-month low.
The Flash Eurozone Manufacturing PMI in August also came in at 46, but this index moved higher from a 45.1 reading in August.
For the manufacturing index, 46 represents a six-month high.
The Manufacturing PMI Output Index for the eurozone reached a five-month high at 45.5, which follows a reading of 44.4 in August.
Markit said the decline in output "reflected an accelerated rate of loss of new business -- the largest monthly fall since May 2009."
In Germany, the largest economy in Europe, the rate of output decline slowed and "the rate of loss of new orders also eased," Markit said. In France, the second largest economy in Europe, output and new orders "both (fell) at the fastest rates since April 2009," the research firm said.
"The Eurozone downturn gathered further momentum in September, suggesting that the region suffered the worst quarter for three years," said Markit Chief Economist Chris Williamson.
"The flash PMI is consistent with GDP contracting by 0.6 percent in the third quarter and sending the region back into a technical recession," he said.
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