Toney replaced Feras Al-Brikan in the 65th minute at Hazza bin Zayed Stadium on Monday and hit both his goals in a four-minute spell to give Al-Ahli a fifth win in a row in the competition and guarantee their place in the next phase.
Cristiano Ronaldo netted a brace in Al-Nassr's 3-1 win over their Qatari hosts Al-Gharafa, while Iran's Esteghlal drew 0-0 with Pakhtakor from Uzbekistan, and Persepolis were held to a 1-1 draw by Al-Rayyan in Doha.
Teams finishing in the top eight in the 12-team leagues in west and east Asia progress to the knockout rounds in March.
Al-Ahli have confirmed their place with three games remaining in the league phase.
Toney broke the deadlock with 20 minutes remaining when he headed Riyad Mahrez's free kick past Khalid Eisa.
Four minutes later he doubled the advantage when he combined again with the former Manchester City winger to slide in the second.
Defending champions Al-Ain had picked up only one point from four games before hosting Al-Ahli, and Alejandro Romero's goal three minutes into injury time gave new coach Leonardo Jardim and his team hope of a late comeback.
But Al-Ahli held on to move to the top of the western standings, three points ahead of compatriots Al-Hilal, who next face Qatar's Al-Sadd.
Al-Ain remain rooted to the bottom on a solitary point with three games remaining.
Ronaldo was a frustrated figure in the opening 45 minutes of Al-Nassr's clash with Al-Gharafa at Al-Bayt Stadium, but headed in the opener inside the first minute of the second half to send his side on their way to victory.
Angelo Gabriel rounded goalkeeper Sergio Rico to score the second 12 minutes later, before Ronaldo hit the third in the 64th minute.
Al-Nassr moved to 13 points from their opening five games, despite Joselu's late consolation for the home side.
Farshad Faraji's header put Persepolis ahead in the 17th minute against Al-Rayyan, who levelled via Achraf Bencharki 12 minutes into the second half to leave both teams facing a battle to make it into the knockout rounds.Â
