Shahzad also made history by scoring two 50s in two different international matches on the same day and became the first ever player in the world to have the record.
According to reports, Kohli was previously the record of scoring maximum three 50s in a single tournament.
However, Shahzad helped the Afghan team to win the Desert T20 Challenge with his four 50s in the tournament.
Kohli had set the record ICC World Twenty20 which was held in India last year.
Afghanistan played the semi-final match against Oman on Friday and defeated them 8 wickets where Shahzad scored 80 runs.
The final match of the tournament was held hours after the Afghan team defeated Oman where Shahzad scored 52 runs and helped defeat Ireland by 10 wickets.
The final match victory was Afghanistan’s fifth consecutive win in the tournament following back to back wins in group matches against Ireland, United Arab Emirates, and Namibia.
The final match of the tournament was played at Dubai International cricket stadium.
The Afghanistan is currently holding the champion status of the 2016/2017 Desert Twenty20 Challenge.