Pakistan installed the system on a trial basis in January 2007 to try and control illegal cross-border traffic at Chaman, 100 kilometres (60 miles) from Quetta, the main town in insurgency-wracked Baluchistan province.
But on the second day, thousands of Afghan tribesmen attacked the border gates, forcing authorities to close the crossing. The protest was against the biometric system, and a Pakistani plan to fence and mine parts of the border.
Further protests saw Pakistan to shelve the system.
"We have decided to reactivate the biometric system. I will inaugurate it on November 30, next month," Malik told reporters in Chaman.
"Both Pakistan and Afghanistan need this system. It is necessary to keep an eye on everyone crossing the border and to stop illegal immigrants," he added.
The system is designed to replace the previous permit system, by issuing border passes to people after recording their fingerprints, retinas or facial patterns for identification.-AFP