The tepid session followed a rise on most major overseas markets, with sentiment boosted by higher oil prices and as US consumer confidence in March reached its highest level in nearly 16 years.
More than 1,500 of nearly 2,000 firms on the Topix were trading ex-dividend Wednesday.
That means investors who buy shares today are not entitled to the next dividend payment. Many Japanese stocks trade ex-dividend on the same day in March and September.
However, exporters were supported by a drop in the yen, which inflates their profitability.
The dollar was at 111.16 yen in Asian trade, up from the mid-110 yen level Tuesday.
"While the ex-dividend trading pressured selected shares, the positive impact of the weak yen limited selling," Toshikazu Horiuchi, a broker at IwaiCosmo Securities, told Bloomberg News.
Tokyo's benchmark Nikkei 225 index edged up 0.08 percent, or 14.61 points, to finish at 19,217.48 while the broader Topix slipped 0.18 percent, or 2.76 points, to end the day at 1,542.07.
Toshiba closed 1.01 percent higher at 219.4 yen after reports that its board had approved a plan to place its US nuclear unit Westinghouse in bankruptcy protection.
After markets closed, both firms said Westinghouse has made a Chapter 11 filing in a US court, which temporarily shelters struggling firms as they try to restructure their affairs and debts.
Kansai Electric Power jumped 8.22 percent to 1,388.5 yen after an appeals court ruled Tuesday that a pair of its nuclear reactors, halted by a lower court order, can be restarted.
Toyota was down 1.51 percent to end the day at 6,124 yen while rival Honda fell 0.96 percent to 3,436 yen.