The administration said the two sanctioned officials - Turkey's Minister of Justice Abdulhamit Gul and Minister of Interior Suleyman Soylu - both played leading roles in the organizations responsible for Brunson's arrest and detention.
The White House announced that the U.S.is imposing sanctions on Turkey's minister of justice and minister of the interior over their country's treatment of the Rev. Andrew Brunson.
"Pastor Brunson's unjust detention and continued prosecution by Turkish officials is simply unacceptable", said Treasury Secretary Steven Mnuchin in a statement.
Brunson was held for almost two years in prison on terror-related charges before he was moved last week to house arrest.
US pastor Andrew Brunson reacts as he arrives at his home after being released from the prison in Izmir, Turkey July 25, 2018.
American officials believed that a deal was in place to free Brunson, but when he was moved to house arrest on July 26, Trump and Pence met and decided that sanctions are in order to force the issue.
Speaking in Ankara, Mr Erdogan said Turkey would not make compromises regarding the independence of the judiciary, and said the remarks of the "evangelist, Zionist mentality" in the U.S. was unacceptable.
"We've seen no evidence that Pastor Brunson has done anything wrong", she said.
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US State Department spokeswoman Heather Nauert has also called the detention "unjust", adding, "Turkey knows our position well".
The Turkish Foreign Ministry said in response to the sanctions that the United States was trying to interfere in the Turkish judicial process.
US officials, for their part, show no inclination to accede to their North Atlantic Treaty Organisation ally's demand, either.
Brunson's next hearing is October 12.
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.
Turkish President Recep Tayyip Erdogan accused his American counterpart of waging "psychological warfare" against Turkey over the pastor and warned that the USA may lose "a strong and honest ally" in Turkey.
Brunson was accused of helping supporters of Fethullah Gulen, the USA -based cleric who Turkish authorities say masterminded the 2016 coup attempt against President Tayyip Erdogan in which 250 people were killed.
In Ankara, Turkey called on the U.S.to reverse its decision and promised to "respond in kind without delay" against what it described as an aggressive stance by the Trump administration.
The White House has not specified what sanctions might be imposed on Turkey.