The visitors took the lead after 14 minutes of the quarter-final first leg when Al Wehdat failed to deal with a long ball, allowing Hasan Karim to score.
But Duhok were then reduced to 10 men when defender Khalid Mousheer was dismissed for deliberate handball in the box, only for Mahmoud Shalabayeh to miss the penalty.
The Jordanians did level in the 31st minute when Duhok's Berhan Sahyuni also handled in the area but this time Hasan Abdel Fatah converted from the spot.
Substitute Abdullah Deeb then put Al Wehdat in front in the second half with a composed finish before Shalabayeh netted the third with five minutes to go after exchanging passes with Monter Abu Amara.
Abel Fatah got on the end of Amir Deeb's cross to grab the fourth goal and Shalabayeh completed the scoring in stoppage time after latching on to Abu Amara's through-ball.
Arbil also look set to reach the last four after they came away from Persipura Jayapura with a 2-1 victory.
The visitors took the lead in the 18th minute when Nabeel Sabah was given time and space to blast home and doubled their lead with 20 minutes to go when Muslim Mubarak tapped home Luay Salah's pass.
Zah Rehman's powerful strike from just outside the box with eight minutes to go kept the Indonesians' hopes alive for the second leg.
Ivan Boskovic slotted home two minutes after the break to give Nasaf a crucial 1-0 triumph at Chonburi.
Finally, Rogerio's 75th-minute strike ensured Kuwait SC will travel to Muang Thong United with a one-goal advantage in two weeks' time.