Flavio Da Silva converted the 39th-minute spot-kick after a lengthy delay while the visitors protested despite big-screen replays showing the ball striking the arm of captain Ahmed Mansour.
Algerian Abderrahim Deghmoum equalized on 57 minutes in Polokwane only for Chiefs to regain the lead three minutes later through an Aden McCarthy tap-in.
The result left Chiefs with a bitter-sweet victory as they needed to win 1-0 or by at least two goals to ensure qualification for the quarter-finals from Group D on head-to-head records.
While Chiefs were edging Masry, Zamalek of Egypt suffered a shock 1-0 away loss to ZESCO United of Zambia in Ndola, where Chadian Amine Hiver converted a second-half penalty.
The results set up an intriguing final round on Saturday with Zamalek hosting Chiefs and Masry having home advantage over ZESCO.
Chiefs have 10 points, Zamalek eight, Masry seven and already-eliminated ZESCO three with two quarter-finals places on the line.
The number of qualifiers for the knockout stage grew from two last weekend to four after Chabab Belouizdad of Algeria and AS Otoho of Congo-Brazzaville secured the Group C slots.
Belouizdad retained first place thanks to a 1-0 win over Singida Black Stars of Tanzania in Zanzibar City. Abdennour Belhocini scored the match-winner after just two minutes.
Both teams finished with 10 men after Mohamed Ben Hammouda of Belouizdad on the hour mark and Abdulmalik Zakaria deep in added time were sent off after both had been booked twice.
Otoho outplayed South African visitors Stellenbosch 3-0 with a Pomi Nzaou goal followed by a brace from Klegnime Kone.
Belouizdad have 12 points and Otoho nine ahead of their meeting in Algeria on Sunday. Singida and 2025 Confederation Cup semi-finalists Stellenbosch have four points each.
Group B leaders Wydad Casablanca of Morocco left it late to beat Nairobi United 1-0 in the Kenyan capital with substitute Wissam Ben Yedder netting in the 89th minute.
Wydad hold a three-point lead over Maniema Union from the Democratic Republic of Congo and AZAM of Tanzania. Nairobi have struggled in their African debut, suffering five straight losses.
Leaders USM Alger of Algeria and Olympique Safi of Morocco, who qualified from Group A last weekend, won 3-2 over San Pedro and 2-1 against Djoliba, respectively.
