The accused included - Aseemanand, Lokesh Sharma, Kamal Chauhan and Rajinder Chaudhary.
Naba Kumar Sarkar aka Swami Aseemanand the prime accused in the case was granted bail by the Punjab and Haryana High Court in 2015.
The blast in the India-Pakistan train took place near Panipat in Haryana on February 18, 2007, when it was on its way to Attari in Amritsar, the last station on the Indian side. It led to led to the death of 68 passengers.
Before pronouncing the verdict, NIA special judge Jagdeep Singh dismissed the plea filed by a Pakistani woman for examining some eyewitnesses from her country.
"The court ruled that the plea of the Pakistani woman was devoid of any merit," Malhotra said.
The blast had ripped apart two coaches of the cross-border train.
The Haryana police registered a case, but the probe was handed over to the National Investigation Agency in July 2010.
The NIA filed a charge sheet in July 2011 against eight persons for their alleged roles in the terror attack.
Of the eight, Swami Aseemanand, Lokesh Sharma, Kamal Chauhan and Rajinder Chaudhary appeared before the court and faced trial.
Sunil Joshi, the alleged mastermind of the attack, was shot dead near his home in Madhya Pradesh's Dewas district in December 2007.
The three other accused -- Ramchandra Kalsangra, Sandeep Dange and Amit -- could not be arrested and were declared proclaimed offenders.
Aseemanand was out on bail, while three others were in judicial custody.
The NIA had charged the accused with murder and criminal conspiracy, and under the Explosive Substances Act and the Railways Act.