As per EFL rules, Wednesday now face an automatic deduction of 12 points and could face further sanctions.
The 12-point deduction leaves the South Yorkshire club at the bottom of the Championship table, on -6 points after 11 matches.
Wednesday had previously been charged with multiple breaches of regulations over the late payment of players’ wages.
Earlier this week, thousands of supporters boycotted their home defeat to Middlesbrough in protest against Dejphon Chansiri's ownership.
Even British government ministers have joined calls for Chansiri to sell Wednesday.
Culture secretary Lisa Nandy told a committee of MPs last month she was “extremely concerned about the current ownership and the lack of willingness to sell the club and invest in the club”, adding that she had been discussing the issue “very closely with local MPs”.
“The government is keeping a very close eye on it, and our message to those owners is that change is coming,” she said.
The Sheffield Wednesday Supporters’ Trust described the club filing for administration as “one of the most bittersweet days in our club’s proud 158-year history”.
“Entering administration was the inevitable outcome of years of financial mismanagement, a lack of accountability and repeated failures to engage credible buyers,” the Trust said.
“Administration is not to be celebrated. It needn’t have ended this way. But we are overjoyed to have Dejphon Chansiri out of our club for good.”
Wednesday's next match is against Oxford United, who are also in the relegation zone, on Saturday.