The Tunisian referee gave a straight red card to Dharles Kalonji from the Democratic Republic of Congo team on 36 minutes when most in the Alexandria crowd expected a yellow.
Already on the back foot against the Egyptian outfit, V Club held out with 10 men until the 65th minute when Nasser Maher sidefooted a cutback into the net from close range.
The killer second goal in the 79th minute came after Karim Walid appeared to dive rather than be fouled by veteran Cameroonian goalkeeper Nelson Lukong when he won a penalty.
Although Lukong correctly guessed the direction of the spot-kick from Tunisian Ali Maaloul, it had too much power and height and flew into the corner of the net.
A furious Lukong pointed a finger and shouted at the match officials after the final whistle at the 87,000-seat Borg el Arab Stadium on a chilly winter night in the Mediterranean city.
The penalty decision triggered memories of the 2018 final first leg in which Ahly star Walid Azaro, who missed the V Club match through injury, appeared to hoodwink the referee twice.
His apparent dive won a penalty against Esperance from Tunisia and he earned a second spot-kick by claiming a foul when TV replays caught him deliberately tearing his shirt.
Ahly converted both penalties to win 3-1, but lost the return match 3-0 in Tunisia to suffer a second successive final defeat in the premier African club competition.
Losing the title decider cost French coach Patrice Carteron his job and experienced Uruguayan replacement Martin Lasarte made his Champions League debut against V Club.
Ahly, whose last Champions League title came in 2013, trail Simba SC on goal difference in Group D after the Tanzanians trounced Algerian visitors JS Saoura 3-0 in Dar es Salaam.
Including qualifiers, Simba have scored 15 goals in five matches, and they began their second appearance in the group stage with a bang.
Ugandan Emmanuel Okwi put them ahead on the stroke of half-time and a second-half brace from Rwandan Meddie Kagere completed the rout.
Five-time African champions TP Mazembe from DR Congo survived the sending off of goalkeeper Sylvain Gbohouo to defeat Egyptian visitors Ismaily 2-0 and top Group C on goal difference.
Reserve goalkeeper Aime Bakula, who replaced the red-carded Ivorian after 44 minutes, saved a penalty before late Chico Ushindi and Kevin Zatu goals secured victory in Lubumbashi.
Algerians CS Constantine won 1-0 away to Tunisians Club Africain Friday through a late Abdenour Belkheir goal to lie second behind Mazembe in the same section.
In Group B, FC Platinum from Zimbabwe and Orlando Pirates from South Africa fought a 0-0 draw before a capacity 30,000 crowd in Bulawayo.
There was no shortage of effort from the sides in the southern Africa showdown, but both lacked a cutting edge in the final third.
All four clubs in a section completed by Esperance and Guineans Horoya, who drew 1-1 in Conakry Friday, have one point.