However, the qualification prospects of Persepolis hang in the balance following their 0-0 draw in Tehran with an Al Nassr side missing Cristiano Ronaldo, the Iranians climbing up to eighth place ahead of Tuesday's final league phase matches.
A draw for fellow Iranians Esteghlal against Qatar's Al Rayyan on Tuesday, who had their progress confirmed after Monday's results, will take them into the knockout rounds at the expense of their bitter cross-Tehran rivals.
The top eight finishers in both West and East Asia advance to the last 16, with teams due to face off over two legs in March in the next phase. The quarter-finals, semi-finals and final will be played centrally in Saudi Arabia in April and May.
Pakhtakor had only scored twice in their previous seven matches in the competition but striker Brayan Riascos doubled that total single-handedly to earn his side their first win of the campaign.
The Colombian put Pedro Moreira's side in front against the already-qualified Qataris with a close-range finish in the 18th minute, only for Al-Sadd to level through a Hassan Al-Haydos penalty eight minutes before the break.
Eleven minutes after the resumption, though, Riascos netted again, nodding home after Jonatan Lucca's free-kick had looped up invitingly off the defensive wall.
Al Ahli were forced to come back from going behind in Jeddah to an early penalty from former Real Madrid striker Joselu to hand Al-Gharafa a defeat that ends the Qatari side's hopes of advancing.
Joselu scored with six minutes on the clock but Ivan Toney bundled the ball home from close range to level in the 21st minute while Roberto Firmino gave the home side the lead when he slid in to score 13 minutes later.
An error from goalkeeper Sergio Rico allowed Galeno's rising shot through his hands for Al Ahli's third with a minute left in the half and Riyad Mahrez's penalty added to Al Ahli's cushion before Yacine Brahimi's 80th-minute consolation spot-kick.
The win moved Al Ahli into top spot in the standings, three points clear of compatriots Al Hilal, who meet Al Wasl of the United Arab Emirates on Tuesday.
Defending champions Al Ain, who had already been eliminated after losing to Al Rayyan earlier in the month, ended their campaign with a sixth defeat and bottom of the standings following a 2-0 loss against Iraqi outfit Al Shorta in Baghdad.