The 6 week-old suffered a cardiac arrest and was rushed to hospital on Monday but he died a few hours later, the autopsy revealing liquid in his lungs.
Prosecutors have opened a manslaughter probe against the priest in the northeastern city of Suceava.
An online petition calling for changes to the ritual had gathered more than 56,000 signatures by Thursday evening.
"The death of a newborn baby because of this practice is a huge tragedy," said a message with the petition. "This risk must be ruled out for the joy of baptism to triumph."
One internet user denounced the "brutality" of the ritual and another criticised the "stubbornness of those who think that it is the will of God" to maintain it.
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