The Pentagon's move, combined with worries about Syria and North Korea, sent investors to the sidelines, said JJ Kinahan, chief market strategist at TD Ameritrade.
"People are saying 'Let's take some risk off the table,'" he said. "With what's going on in geopolitics, who knows what can happen" over the long weekend.
The Dow Jones Industrial Average dropped 0.7 per cent to end the session at 20,453.25.
The broad-based S&P 500 shed 0.7 per cent to close at 2,328.95, while the tech-rich Nasdaq Composite Index fell 0.5 percent to 5,805.15.
Markets are closed Friday for Good Friday.
Petroleum-linked shares were big losers in an apparent round of profit taking following gains earlier in the week. Dow members Exxon Mobil and Chevron lost 1.5 percent and 2.6 percent, respectively, while Halliburton slid 1.9 percent.
Wells Fargo slumped 3.3 percent after reporting flat earnings that missed analyst expectations amid the continued effects of the bank's fake accounts scandal.
Rivals JP Morgan Chase and Citigroup also saw their share prices dip despite reporting better-than-expected first-quarter earnings. Citigroup lost 0.8 percent and JP Morgan Chase 1.2 percent.
Tesla Motors gained 2.4 percent after chief executive Elon Musk said the electric car startup was set to launch its first semi-truck in September, moving for the first time into that segment.