The pastor called off the burning at the last minute after outcry from political and religious leaders the world over and promised that he would not burn any Korans.
However, the pastor held a mock trial and execution of a Koran at his small church in Gainesville, Florida, last month. During the stunt, the Koran was found "guilty" of crimes and was set on fire by fellow church pastor Wayne Sapp under Jones' supervision.
The Koran burning prompted protests by Muslims in Pakistan in which they burned the American flag and shouted slogans against the US.
Last week, St Thomas church in Wah Cantt was attacked by a group of Muslims who tried to break through the front door and set fire to the building.
When they were unable to break in, they fled the scene, according to Spero News.
The church's pastor, Father Yousaf, said: "This is a reaction of the desecration of the Koran in Florida. Although the Catholic Church has officially condemned the incident and we have also displayed a banner outside the church condemning the incident, still the innocent people are facing the consequences."
Wah Cantt is close to Pakistan's only ammunitions factory and sits within an area with a strong military presence and barriers at the entry points.
The attack has raised questions about the safety of Christians in Pakistan, who are fearing for their lives after the recent assassinations of Punjab Governor Salman Taseer and Minorities Minister Shahbaz Bhatti.
Taseer was shot dead by his own bodyguard, causing many Christians in Pakistan to question the integrity of the police.
According to Spero News, churches in the Wah Cantt area have been advised by police to install security cameras and hire Christian security guards.
The Bishop of Islamabad and Rawalpindi, Rufin Anthony, urged the police to hold the attackers to account.
"We condemn the attack. We had officially condemned Terry Jones from Florida. We have clarified that we are Pakistani Christians, not Americans," he said.
Nasir Saeed, the coordinator of the Centre for Legal Aid, Assistance and Settlement in the UK, a charity which provides free legal support to Christians in Pakistan, agreed that the attack on the church was a direct consequence of Terry Jones' actions.
"Any actions by the West that are against Islam – or even perceived to be against Islam – inevitably lead to the worst consequences possible for innocent people, particularly Christians, living in majority-Muslim countries," he said.
"We fear that ill-sentiment towards Christians in Pakistan could now escalate and lead to the destruction of life and our places of worship."
He called upon the Pakistani government to take action to stop the killing of Christians and attacks on their churches.
"We urge the government of Pakistan to take the appropriate action and ensure that churches and other places of worship are protected."
St Thomas is the second church to be attacked in a matter of weeks. Two Christians were killed last month when a group of Muslim youths opened fire on a congregation as they left a prayer meeting at a Salvation Army church in Hoor Camp.
The victims were a 47-year-old father of four and a 21-year-old newly-wed.