Mr Johnson made the comments on Wednesday during a press conference. He was asked if Mr Biden's presidency was "God's will."
"It must have been God's will," Mr Johnson, a Southern Baptist Christian, said.
Mr Bannon said the House Speaker's comments would make "heads blow up."
"Yo, dude, he's an illegitimate president!" Mr Bannon said, before repeating Mr Trump’s falsehoods about the results of the 2020 presidential election. "Have you lost your freaking mind? This election was stolen."
He continued to rant, insisting that somehow Mr Biden managed to ascend to the presidency in defiance of the Almighty.
"Joe Biden's not a legitimate president of the United States," he continued. "No to the Speaker. So no, God did not raise him up."
He said he refused to hear any further "happy talk" from Mr Johnson, before airing his support for a government shutdown.
"The framers and the founders gave you the power of the purse. Shut it down," he said.
Steve Bannon reacts to Speaker Johnson stating that Joe Biden becoming president was the will of God. pic.twitter.com/xhdB72cUcV
— PatriotTakes 🇺🇸 (@patriottakes) January 17, 2024
Mr Johnson has found himself stuck in a position similar to the one that led to the downfall of former House Speaker Kevin McCarthy; a government shutdown will occur if a continuing resolution (CR) is not passed to keep it funded. Maga Republicans do not want Mr Johnson to support a CR, but not doing so will grind the government to a halt.
Congressman Matt Gaetz cited a deal Mr McCarthy made with Democrats to keep the government funded as the primary reason he moved to vacate his seat.
After calling for the government shut down, Mr Bannon suggested that men like Mr Johnson would somehow lead to the mass conversion of American men to Islam.
"Guys like Johnson are gonna lead to mass conversions to Islam by young men," he said. "Wait for it. If that's what Christianity gives you, if that's what it gives you as far as being a warrior when you roll over to your enemies, disgusting."
Despite Mr Bannon's protests, Mr Johnson's comments are not necessarily an endorsement of Mr Biden. Some Southern Baptists hold Calvinist views of God, which include the belief that God is sovereign. Therefore, nothing can happen outside of God's will, good or bad, including Mr Biden's presidency. In that theology, the fact that Mr Biden is the president is evidence God willed his victory.