The benchmark January soybean contract settled down 6-3/4 cents at $9.86-1/2 a bushel, just above its 200-day moving average near $9.86.
Commodity brokerage INTL FCStone late on Tuesday raised its estimate of the average US 2016 soybean yield to a record 52.8 bushels per acre, from 52.5 last month.
Additional pressure stemmed from declines in crude oil prices, equities and the dollar tied to uncertainty about the outcome of next week's US presidential election.
Funds hold a net long position in CBOT soybean futures, leaving the market vulnerable to bouts of long liquidation.
Soy market underpinned by export demand. The USDA said private exporters in the last day sold 132,000 tonnes of US soybeans to China for delivery in the 2016/17 marketing year.
The CME Group reported 100 deliveries against the CBOT November soybean contract, the first of the cycle.
CBOT December soymeal closed lower on spillover weakness from soybeans and oil/meal spreading.
CBOT December soyoil closed higher on oil/meal spreading and spillover support from allied Malaysian palm oil futures.