The two officials targeted by sanctions "played leading roles in the organizations responsible for the arrest and detention" of Brunson, the US Treasury's Office of Foreign Assets Control (OFAC) said in a statement.
"As a result, any property or interest in property of both ministers within United States jurisdiction is blocked and U.S. persons are generally prohibited from engaging in transactions with them", she said.
Although the statement did not detail what sanctions Turkey will retaliate, but it's expected that similar sanctions will be imposed on Attorney General and Secretary of Interior of the US administration.
The Turkish currency dropped to an all-time low against the dollar following the announcement of the sanctions, trading at just over 5 lira against the dollar.
Speaking to reporters on Wednesday, Ms Sanders said: "We've seen no evidence that Pastor Brunson has done anything wrong".
President Donald Trump had threatened Ankara with "large sanctions" if Brunson is not released.More news: Spy agencies suspect North Korea building new missiles
Brunson was accused of helping supporters of Fethullah Gulen, the US -based cleric who Turkish authorities say masterminded the 2016 coup attempt against Erdogan in which 250 people were killed.
The Treasury Department will place sanctions on Turkey's minister of justice and minister of interior, White House Press Secretary Sarah Sanders confirmed at a press briefing.
Jay Sekulow, chief counsel of the American Center for Law and Justice, which represents Brunson's family, said the ACLJ was not surprised that the appeal was denied.
Relations between Turkey and the United States have been tense over multiple issues including American support for a Syrian Kurdish militia who Turkey claims are terrorists as well as the failure to extradite US-based Muslim preacher Fethullah Gulen.
Brunson, who has lived in Turkey for more than two decades, faces up to 35 years in jail if found guilty of the charges, which he denies. Ozkan had been detained by Israel on terror-related charges, but was deported this month.
Secretary of State Mike Pompeo said the Turkish government refused to release Brunson "after numerous conversations between President Trump and President Erdogan", along with his conversations with Turkish Foreign Minister Mevlut Cavosuglo.
The move failed to secure Brunson's release.