The second assailtant was captured soon after, Reuters reported.
The gunman was also killed, along with at least one police officer, officials said.
Egyptian authorities are calling the attack a foiled attempt - as they say the gunmen had explosives that could have made the attack even deadlier.
Police have stepped up security measures around churches ahead of the Coptic Christmas celebrations on Jan 7, deploying officers outside Christian places of worship and setting up metal detectors at some of the bigger churches.
Five terrorists, including one with attached explosives to the body, attacked a church near Cairo on Friday morning, according to the newspaper Al-Watan. President Abdel-Fattah el-Sissi has personally chaired meetings with his top security chiefs in recent days to discuss security during New Year's Eve and the Orthodox Christmas.
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At least one militant was killed in a shootout outside a church south of Cairo on Friday, state-media reported.
The interior ministry said in a statement in the afternoon that it arrested an attacker who attempted to drive through security forces outside the church armed with a machinegun, ammunition and a bomb that he meant to detonate in the church. It also said there was a separate attack on a store in the same neighborhood of Helwan that killed two Copts.
IS had claimed a suicide bombing of a Cairo church in December 2016 followed by bombings of two churches north of the capital in April. The officials stated that a gunman fired upon people outside the church.
"The security forces frustrated an attack on church in Mar Mina Church the Helwan district", said the interior ministry statement.
Cellphone footage posted on social media appeared to show the bearded gunman wearing a bulky ammunition vest sprawled on a street, barely conscious, as people restrained his arms and then handcuffed him. Authorities have closed off the area around the church.