A total of 523 banks took a record 489.2 billion euros ($641 billion) on which the ECB will charge annual interest of just one percent over three years.
Until now, the ECB has lent for a maximum of one year and the new arrangement is part of a series of unprecedented measures to keep credit flowing in Europe at a time when banks are increasingly wary of lending to each other due to the debt crisis.
The Nikkei index at the Tokyo Stock Exchange slid 30.44 points to 8,429.54. The Topix index of all first section shares rose 0.21 percent or 1.49 points to 724.19.
Ongoing concerns over potential eurozone sovereign debt downgrades, as well as instability in North Korea, could prevent market participants from buying aggressively towards the year end, dealers said.
"Buying into major stocks doesn't last these days," Hideyuki Ishiguro, supervisor of investment strategy at Okasan Securities, told Dow Jones Newswires.
"Trading is likely be thin as some market participants are already away this week," he said.
US stocks markets were mixed overnight after Tuesday's strong gains, with the Nasdaq dragged lower on poor Oracle earnings and other indexes finding little direction in holiday-thinned trade.
By the close the Dow Jones Industrial Average reached 12,107.74 points, up just 4.16 points or 0.03 percent. The S&P 500 was up 0.19 percent, or 2.42 points to 1,243.72.
The Nasdaq was down 25.76 points or 0.99 percent to 2,577.97, largely dragged down by Oracle.
The euro stood at $1.3038, down from $1.3188 in New York Wednesday, and at 101.74 yen, compared with 101.88 yen in New York.
The dollar was at 78.04 yen, almost unchanged from 78.05.