Police said an explosion happened as two people tried to enter the church on Palm Sunday, the first day of Easter.
A destroyed motorbike and body parts were found at the scene and police said the two attackers had died.
Militant Islamists have attacked churches in the past but no group has yet said it was behind the bombing.
Religious Affairs Minister Yaqut Cholil Qoumas condemned the attack and urged police to increase security measures at places of worship.
"Whatever the motive is, this attack cannot be justified by any religion because it only does harm to other people," he said.
The explosion happened at about 10:30 local time (03:30 GMT) at the end of a service for Palm Sunday.
"There were two people riding on a motorbike when the explosion happened at the main gate of the church - the perpetrators were trying to enter the compound," National Police spokesman Argo Yuwono said.
A priest at the church, Father Wilhemus Tulak, told Metro TV that security guards had tackled one suspected bomber.
The attacker, he said, arrived by motorbike and tried to get into the church.
Police said at least 14 people were injured, including the church officials who stopped the attackers from entering the grounds of the cathedral.
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