The Saudi outfit came into the second leg with a 3-0 advantage, but Lee Myung-joo's first-half strike may have given them cause for concern.
Nasser Al Shamrani - star of the first leg - pulled the visitors level in the 65th minute, before Al Ain's Asamoah Gyan was dismissed for a two-footed challenge.
Jires Kembo-Ekoko nevertheless touched home from close range to give Al Ain a second-leg lead, but the aggregate score proved too big a mountain to climb.
Both goalkeepers almost got caught hesitating on the ball in the early stages, but it was not long before Al Ain made a dent in Al Hilal's lead.
Lee managed to evade his marker at an Omar Abdulrahman free-kick to put himself in space and nod home from close range in the 10th minute.
Gyan saw a header well saved by goalkeeper Abdullah Al Sudairy, before Digao sent the ball inches wide at the other end when Waleed Salem failed to deal with a set-piece.
Al Shamrani prodded home an important away goal in the 65th minute to leave Al Ain needing an unlikely four goals to reach the final, and any slim chances of a turnaround appeared over when Gyan saw red five minutes later.
The Ghana captain made a reckless scissor challenge on Salem Al Dawsari and refused to leave the field for a long period after being given his marching orders.
An irate Gyan was eventually ushered down the tunnel, before his side pulled back another goal through Kembo-Ekoko.
Mohamed Ahmad chipped a cross into the six-yard box from a tight angle, with the Frenchman touching the ball into the net on the line.
Al Ain continued to press, with Lee having an effort cleared off the line five minutes from time, but 2-1 is how it remained, with Al Hilal going on to face Seoul or Western Sydney Wanderers in the final.
