The judge described the attack on the church in suburban Kuala Lumpur as "appalling and despicable".
"It strikes at the very foundations and tenets of a civilised society," she told the pair, Raja Mohamad Faizal Raja Ibrahim, 24, and Raja Mohamad Idzham Raja Ibrahim, 22.
A third man was acquitted over the attack.
The convicted pair can be sentenced to 20 years in prison each under the law.
The attacks, in which no one was hurt, were triggered by a Muslim court overturning a government ban on non-Muslims using the word "Allah" in their literature, last December.
The decision led to the Herald, a Roman Catholic newsletter, using the term to refer to God in the Malay language.
The judge since suspended the implementation of the ruling, after the government appealed and the Roman Catholic church agreed to the suspension.
Protests were held by Muslim groups against the overturning of the ban at the time.
Muslims in Malaysia argue that the "Allah" is exclusive to Islam, and its use by Christians would confuse Muslims.
But Catholic church officials say that for Christian indigenous tribes in East Malaysia, who are the main readers of the Herald's Malay-language edition, "Allah" is the only word they have known for God for decades.