Pastor Mark Burns from South Carolina led prayers at the Republican National Convention where Mr Trump was officially endorsed as their candidate for president.
Before beginning his prayer Pastor Burns warned that "our enemy is not other Republicans, but is Hillary Clinton and the Democratic Party".
He said: "We are electing a man in Donald Trump who believes in the name of Jesus Christ".
His prayer was quickly condemned as "inappropriate" by a leading American interfaith organisation while leading conservatives took to Twitter to criticise.
Pastor Burns went on: "Let's pray together. Father God, in the name of Jesus, Lord, we're so thankful for the life of Donald Trump.
"We are thankful that you are guiding him, that you are giving him the words to unite this party, this country, that we together can defeat the liberal Democrat party.
"To defeat every attack that comes against us, to protect the life of Donald Trump, give him the words, give him the space, give him the power and the authority to be the next President of the United States of America, in Jesus' name, if you believe it, shout Amen!"
Interfaith Alliance President Rabbi Jack Moline said he had "rarely heard a more inappropriate contribution to political proceedings".
He said: "The idea that a member of the clergy would invoke his God's name and, in the next breath, declare the candidate from the other party to be the enemy seems to be an attempt to replace 'nomination' with 'ordination.'
"However, invoking religion to launch such attacks devalues faith and disrespects the people of the United States who are hoping for a debate on the issues, not an 'ex cathedra' pronouncement. Republican delegates should decline to respond 'amen.'"
The man who led faith issues on former candidate Marco Rubio's campaign said the prayer was "shameful".
It was a "disgusting and disturbing misuse of God's name and lies," he said.