Corn was also flat on harvest pressure and limited demand, while wheat firmed in a modest rebound from two days of declines.
Grain markets have been focused on US-China trade developments as the two countries work to end their bruising trade war that has clipped exports of US crops.
Beijing on Tuesday offered major Chinese and international soybean processors waivers that would exempt the companies from steep tariffs on imports of up to 10 million tonnes of US soybeans, according to two people briefed on the matter.
The news, however, failed to unleash a torrent of soybean buying by the world's top soy importer.
The US Department of Agriculture (USDA) on Wednesday confirmed 128,000 tonnes in soybean sales, valued at around $49 million at current US export prices, to an undisclosed buyer that was widely believed to be China.
The small volume would be a fraction of China's pre-trade-war US soy purchases of more than $12 billion a year.
"The lack of confirmation of bigger purchases is a little negative to the market," said Terry Reilly, senior commodities analyst with Futures International.
Improving harvest weather in the United States also weighed on corn and soybean futures after late planting and delayed development of both crops have underpinned prices this season.
"The slow harvest progress is a little bit supportive, but the weather has improved and we expect it will continue to improve over the next week," Reilly said.
Chicago Board of Trade (CBOT) November soybeans ended down 1/4 cent at $9.33-3/4 a bushel while December corn was down 1/4 cent at $3.87-3/4 a bushel.
CBOT December wheat gained 2-3/4 cents to $5.20-3/4 a bushel.
Wheat was underpinned by crop concerns in some key exporting nations and strong global demand for the grain.
Futures gains, however, were tempered by stiff competition in export markets that has limited sales of US supplies.
Algeria bought about 600,000 tonnes of milling wheat, likely sourced from France, in a tender on Tuesday.