The Red Knights were the favourites on their home turf following their 1-0 first leg win in August, and despite some stiff late resistance managed to book their slot in the last four where they meet Saudi Arabia's Al Hilal.
Former Benfica player Rodrigo Lima put Al Ahli ahead in the 26th minute with a powerful low drive from 25 yards after Ahmed Khalil had done the spadework on the left flank and crossed to him.
Khalil, who proved hard to contain, then scored from the spot in the 50th minute with a delicate chip over Naft goalkeeper Alireza Beiranvand after he was brought down in the penalty area.
Naft reduced the margin two minutes later through Vahid Amiri who scored from close range after Waleed Abbas bungled a clearance.
Both teams then missed a couple of chances but Al Ahli held on to stay on course for the continental title.
Earlier, substitute Koki Yonekura snatched a winner deep into stoppage time as Japan's Gamba Osaka stunned South Korea's Jeonbuk Motors 3-2 to reach the semi-finals.
Gamba, the 2008 Asian champions, will face China's Guangzhou Evergrande in the last four after Luiz Felipe Scolari's side dumped J-League rivals Kashiwa Reysol out of the competition on Tuesday.
Jeonbuk looked to be going through on away goals following a scoreless first leg in Korea when Spaniard Urko Vera's header two minutes from time sent the away fans into raptures -- while Gamba's players slumped to the turf in despair.
But last year's Japanese treble winners, who were missing Japan striker Takashi Usami through suspension, hit back in dramatic circumstances, with Yonekura smashing home a left-foot strike in the fourth minute of injury time at Expo stadium.
Jeonbuk, who won Asia's premier club competition in 2006, began brightly and went ahead through a Leonardo penalty after 13 minutes.
Their lead was short-lived after Brazilian striker Patric pounced from close range just moments later before Shu Kurata rifled home from the edge of the box midway through the second half.
Vera's late goal frayed Gamba's nerves before Yonekura broke Korean hearts and sealed a famous victory for the home side.