The blaze had burned through the roof of the Shiloh Baptist Church at 95 Murray St., within minutes of erupting around 3:10 a.m.
The fire reached four alarms and was under control around 6 a.m.
Shiloh Baptist Church was founded in 1879, its Facebook page says.
Parishioners and community members sent encouraging words to Pastor William Ingram on Facebook.
"Please keep the Shiloh Baptist Church , Elizabeth, New Jersey in prayer and Pastor William Ingram," one person wrote.
"A fire destroyed the building, but the Body of Baptized Believers will continue to go forth."
Speaking to reporters outside, Ingram called the fire a shock.
"We were anticipating waking up this morning coming to church to worship," he said.
"[But] that’s the nature of life, and you know, that’s why we have faith."
The cause remains under investigation.
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