Al Ain, winners of the trophy in 2024, picked up their third win in a row as Houssine Rahimi scored his fifth goal in three matches with 20 minutes remaining at the Hazza bin Zayed Stadium.
"This competition is important and we need to collect points early on," said the Moroccan forward. "That is what we managed to do in these three matches we have played, earning nine points. This is very important for us."
Ramy Rabia's strike from distance in the 21st minute had put Al Ain in front but Tibor Halilovic curled home Tractor's equaliser 10 minutes into the second half before Rahimi hit the winner.
Al Ahli made a positive start in Jeddah against their Qatari visitors when Ivan Toney gave the defending champions a fourth-minute lead only to see Florinel Coman level eight minutes into the second half.
Seydou Sano's sending-off for a second bookable offence with 13 minutes remaining left Al-Gharafa short-handed and Al Ahli took advantage with Matheus Goncalves hitting the winner four minutes from time.
"We know that our primary focus isn't just being at the top of the table," said Goncalves.
"We have to qualify, and qualify well, so that afterwards we can take advantage of our home matches and get the job done at home."
Julian Quinones scored in the 84th minute with a heavily deflected effort to earn Al-Qadsiah a 1-1 draw with Qatar's Al-Sadd, who took the lead through Akram Afif's stunning strike from distance 10 minutes earlier.
Iraq's Air Force Club picked up their first win of the campaign when Saad Abdul Ameer pounced in the 70th minute to seal a 1-0 victory in Basra over Pakhtakor from Uzbekistan.
The match involving Saudi Pro League champions Al-Nassr and Al-Wasl from the United Arab Emirates was postponed.
The first eight finishers in the league phase in west and east Asia will advance to the knockout rounds, with the quarter-finals, semi-finals and final to be played on a centralised basis in Saudi Arabia in April and May.