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The Buccaneers lost 1-0 away to TP Mazembe of the Democratic Republic of Congo in a clash of former title-holders, but squeezed into the last eight 3-2 on aggregate.
Also through are Zamalek of Egypt, AC Leopards of Congo, Sewe San Pedro of Ivory Coast, Esperance of Tunisia, Recreativo Libolo of Angola and Coton Sport of Cameroon.
VIDEO: TP Mazembe v Orlando Pirates - highlights
Defending champions Al-Ahly of Egypt or CA Bizertin of Tunisia, who clash later on Sunday in Cairo behind closed doors for security reasons, will complete the line-up for the six-round mini-league stage.
Meyiwa, who forced his way into Pirates' starting line-up last season after many years as an understudy, stopped spot kicks from Eric Bokanga on 50 minutes and Tresor Mputu two minutes from time.
But he was helpless to prevent Jean Kasusula scoring after 72 minutes to set up a tense climax in the southern Congolese mining city Lubumbashi as Pirates repulsed continuous attacks.
The only South African winners of the premier CAF club competition were reduced to 10 men late in the opening half when veteran centre-back Lucky Lekgwathi received a harsh straight red card.
Overall success was a massive relief for coach and former South Africa goalkeeper Roger de Sa, who has come under fire from supporters after woeful domestic league form.
Pirates flew to DR Congo having won just one of their last nine PSL matches and they trail leaders and arch-rivals Kaizer Chiefs by seven points with three matches to play.
Zamalek, whose five Champions League titles is the second best record behind the seven of Cairo neighbours Ahly, snatched a late 2-2 draw at Saint George of Ethiopia to advance on the away-goals rule after a 1-1 stalemate in Cairo.
Burkina Faso-born striker Abdoulaye Cisse was the two-goal star for the White Knights, opening the scoring after two minutes and levelling with a header two minutes from time.
Shimeles Bekele equalised 15 minutes into the opening half at a packed 30 000-capacity national stadium in Addis Ababa and Isaac Isinde edged the Saints in front just before half-time.
Last-16 losers Saint George, Mazembe, JSM Bejaia and Entente Setif of Algeria, Stade Malien of Mali, FUS Rabat of Morocco and Enugu Rangers of Nigeria drop to the second-tier CAF Confederation Cup.
CAF Champions League last-16, second-leg results this weekend:Addis Ababa
Saint George (ETH) 2 (Bekele 15, Isinde 45) Zamalek (EGY) 2 (Cisse 2, 88)
Zamalek win on away goals after 3-3 aggregate tie
Lubumbashi
TP Mazembe (COD) 1 (Kasusula 72) Orlando Pirates (RSA) 0
Pirates win 3-2
Calulo
Recreativo Libolo (ANG) 3 (Camara 16, Cardoso 32, 74-pen) Enugu Rangers (NGR) 1 (Mba 56)
Libolo win 3-1
Tunis
Esperance (TUN) 1 (Chammam 77-pen) JSM Bejaia (ALG) 0
Esperance win 1-0
Abidjan
Sewe San Pedro (CIV) 0 FUS Rabat (MAR) 0
Sewe win on away goals after 1-1 tie
Bamako
Stade Malien (MLI) 0 Coton Sport (CMR) 0
Coton win 3-0
Setif
Entente Setif (ALG) 3 (Djahnit 21, Delhoum 39, 90+2) AC Leopards (CGO) 1 (Bhebey-Ndey 14)
Leopards win 5-4 on penalties after 4-4 tie
Cairo
Al-Ahly (EGY, holders) 2 (Barakat 47-pen, Moteab 62) CA Bizertin (TUN) 1 (Hadhria 65-pen)
Ahly win 2-1 on aggregate
