The league's other 29 owners had been expected to vote in approval at their quarterly meeting in Paradise Valley, Ariz., on Thursday, but deferred seeking more financial information.
MLB commissioner Bud Selig confirmed the vote was dropped from the agenda because of "economic concerns" that Moorad could not immediately explain. The outstanding issues posed no threat to the deal in the long-term.
But the delay reportedly so angered Padres chairman John Moores that he voted against Selig's two-year contract extension, becoming the sole dissenter in an otherwise unanimous endorsement of the commissioner from the owners.
Moorad owns 49 percent of the Padres, through his group of partners. The former player agent became a minority owner with the Arizona Diamondbacks before buying into the Padres ahead of the 2009 season. He needs 75 percent support from the 29 other owners to finalize his takeover from Moores.
Moorad attempted to seal an "11th-hour" agreement amid Thursday's setback, but failed to satisfy the demands of the ownership committee and executive council.
"We got word that there were these questions and we tried to answer them [Thursday] morning," he said. "But it wasn't possible to work that quickly. I told them I was happy to defer and take it up at a more appropriate time."