Selig said in a statement that he did not believe the estimated $3 billion transaction would have been in the best interest of the Dodgers franchise, adding that the deal would further divert Dodger assets to McCourt's "personal needs."
"We owe it to the legion of loyal Dodger fans to ensure that this club is being operated properly now and will be guided appropriately in the future," Selig said in the statement.
The deal was criticized by some in baseball for being below market value.
The McCourts' agreement called for only $235 million of the $385 million from Fox going to the team - $80 million would have gone toward paying debts, and the $70 million would have gone toward the McCourts and the cost of the divorce settlement.
Frank and Jamie McCourt had reached a settlement on Friday that involved having a one-day trial to determine if the title for the Dodgers goes to Frank McCourt or whether the team should be deemed community property.
But now, the settlement is null and void, and the two need to head back to divorce court.
Frank McCourt said in a statement that Selig's decision was not only disappointing, but also "potentially destructive to the Los Angeles Dodgers and Major League Baseball."
"As Commissioner Selig well knows, this transaction would make the Dodgers financially secure for the long term," McCourt said in the statement.
Frank McCourt has struggled to meet team payroll since the start of the season and without money from a TV deal, Selig could seize control of the Dodgers if McCourt doesn't pay his bills.
The fans have let their absence do their talking for them. Dodgers attendance is down more 7,000 a game - the biggest decline in all of baseball.
"It is disturbing because a team should be the team, and his personal life should be his personal life," said Dodgers fan Jorge Ledesma. "It seems obvious that he pulled a lot of money out of the team coffers for his own personal benefit."
Up next is a June 30 obligation, where deferred compensation for some former players is due. Among them is Manny Ramirez, who is owed nearly $7 million as part of a two-year, $45 million contract he signed with the Dodgers.
The Associated Press contributed to this report.