The winner of the match will play the second eliminator with Peshawar Zalmi on Friday.
Islamabad, winners in 2016 and 2018, were equal on the points table with their rivals in the league phase but finished ahead of Karachi on better net run-rate.
The match will start at 7 pm PST.
Earlier on Wednesday, Quetta Gladiators booked their place in the Pakistan Super League (PSL) 2019 final by securing a 10-run win over Peshawar Zalmi in the qualifier at National Stadium Karachi.
Zalmi, who were chasing a 197-run target set by the Gladiators, managed to score 176 runs by the end of their 20 overs.