The "full closure" will allow inspections of the system's third-rail power cables following an early morning tunnel fire on Monday, Wiedefeld said in a news release.
About 600 jumper cables will be examined along tunnel segments in the system.
The system is due to remain closed at least until Thursday's normal scheduled opening at 5 a.m. "At the conclusion of the inspection process, there may be a need for additional rail service outages," the news release said.
"While the risk to the public is very low, I cannot rule out a potential life safety issue here, and that is why we must take this action immediately," Wiedefeld said. "When I say safety is our highest priority, I mean it. That sometimes means making tough, unpopular decisions, and this is one of those times. I fully recognize the hardship this will cause."
The U.S. Office of Personnel Management said federal agencies in D.C. have option for unscheduled leave or telework. Washington's public schools will remain open Wednesday. In a statement, District of Columbia Public Schools said it is working with Metro to add additional bus service.
Metrorail, which called the shutdown "unprecedented," has six lines and 91 stations.
The shutdown follows an electrical fire involving a cable in the tunnel outside the McPherson Square Station that disrupted service on the Blue, Orange and Silver lines. There were no injuries.
"The investigation into yesterday's cable fire at McPherson Square is ongoing," Wiedefeld said.
But he said the conditions appear "disturbingly similar" to those surrounding a fatal smoke incident in a tunnel near the L'Enfant Plaza stop a year ago.
"Our focus is squarely on mitigating any risk of a fire elsewhere on the system," Wiedefeld said.
Metrobus and MetroAccess service will continue on a regular schedule.
Rep. Chris Van Hollen said the shutdown "is an astonishing admission that safety has not been the priority it needs to be" at the Washington Metropolitan Transportation Authority.
The Maryland Transit Administration said will operate its MARC Train and Commuter Bus services on a normal schedule on Wednesday through Thursday morning.
MARC Bike Cars will run on select Penn Line trains where passengers can only bring full-size, non-collapsible bicycles, the agency said. Spaces are on a first-come, first-served basis.
The following trains will offer bike cars:
•Penn Line morning: Train 511 (5:40 a.m. departure from Perryville/6:25 a.m. departure from Penn Station), Train 413 (6:45 a.m. departure from Penn Station).
•Penn Line evening: Train 634 (4:40 p.m. departure from Union Station), Train 642 (5:50 p.m. departure from Union Station).
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