Campaign posters unveiled by Hofer's anti-immigration Freedom Party (FPÖ) last week feature the phrase "So help me God" alongside slogans like "Norbert Hofer. For Austria with heart and soul".
The party said it chose the religious reference because it reflected "a strong anchorage in Christian and western values".
But the country's three main Protestant churches accused of Hofer of "abusing" the name of God to push a xenophobic agenda.
"God cannot be instrumentalised for personal intentions or political purposes," Bishop Michael Buenker said in a joint statement with other Protestant leaders.
"We consider that mentioning God... to indirectly attack other religions and cultures amounts to an abuse of his name and religion in general."
They added that the Bible's God was universal and defended the weak, poor and vulnerable -- "who today particularly include refugees and foreigners".
The FPÖ rejected the criticism, saying the phrase came "directly from the heart" of Hofer, a lapsed Catholic who joined the Protestant church.
Like populist parties elsewhere in Europe, the FPÖ is currently leading national polls after stoking public fears about record immigration and rising unemployment.
Hofer, often described as the far-right's "friendly face", hopes to become the European Union's first far-right head of state in the December 4th re-run poll.
In the May election, the 45-year-old narrowly lost by just 31,000 votes to independent ecologist Alexander Van der Bellen, 72.
But the result was annulled after Austria's highest court in July upheld the FPÖ's claims of procedural irregularities.
In a further embarrassing twist, the government was last month forced to postpone October's planned re-run after it emerged that the postal vote envelopes were not sticky enough, meaning they could easily be reopened.
Latest polls show the rivals neck-and-neck. The electoral fiasco has left Austria without a president since July 8th when Heinz Fischer stepped down.