"God forgive us - Jesus - we've lost sight of you, we've forgotten you, God, in our country, and we're asking you to forgive us, Jesus," she prayed.
She also prayed for US President Donald Trump and thanked him for "unequivocally" supporting Israel.
"I claim all these things in the powerful, mighty name of Jesus, the one who, at the name of Jesus, every knee will bow, and every tongue will confess, Jesus, that you are Lord, in Jesus' name," Borowicz said.
Johnson-Harrell, whose installation was attended by Muslim family and friends, told the Pennsylvania Capital-Star: "I don't think it was a prayer, I think it was a political statement masked as a prayer.
"I thought that it was laced with Islamophobia and xenophobia.
"It blatantly represented the Islamophobia that exists among some leaders - leaders that are supposed to represent the people. "I came to the Capitol to help build bipartisanship and collaborations regardless of race or religion to enhance the quality of life for everyone in the Commonwealth."
Borowicz has since defended her choice of words.
She told Andrew Bahl from website The PLS Reporter: "That's how I pray every day...I don't apologise ever for praying."
But other lawmakers have criticised Borowicz.
House Minority Whip and fellow Republican Jordan Harris said Borowicz had "weaponized" her prayer.
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