Parreira, coach of the 1994 Brazil World Cup-winning team, refused to reveal why a forward he had battled to get back into a goal-shy Bafana Bafana (The Boys) squad was suddenly totally left out.
The Brazilian, who has been in charge of South Africa since March, said he had not informed McCarthy that he would not be going to the biennial African football showcase.
Questions were raised after the squad was named as to why the joint-leading Bafana scorer with 29 goals had not made a squad to be captained by Blackburn team-mate, defender-cum-midfielder Aaron Mokoena.
Some observers suspected South Africa struck a deal with Blackburn manager Mark Hughes to leave McCarthy out as Premiership clubs brace for a mass exodus of stars for the three-week tournament in west Africa.
When Parreira took over, charged with building a strong squad for the 2010 World Cup hosts, his first serious challenge was to woo temperamental McCarthy out of self-imposed retirement since the 2006 Nations Cup in Egypt.
Youth and experience
McCarthy, who burst into prominence by scoring nine goals at the 1998 Nations Cup in Burkina Faso to help South Africa finish second, claimed he was wrongly accused by national association officials for stirring a bonuses row.
Parreira eventually got his way after a five-minute meeting in England and McCarthy scored on his return against Zambia in Cape Town two months ago to draw level at the top of the goals list with retired striker Shaun Bartlett.
The 23-man squad includes two uncapped players in Orlando Pirates striker Excellent Walaza and Kaizer Chiefs goalkeeper Itumeleng Khune, both 20.
However Parreira did include 33-year-old striker Sibusiso Zuma, who captained South Africa at the last Nations Cup finals in Egypt in 2006.
South Africa, the first of the 16 finalists to name their squad, have been drawn with Angola, Senegal and Tunisia in Group D at the African Cup of Nations finals.
South Africa squad:
Goalkeepers: Rowen Fernandez (Arminia Bielefeld/GER), Moeneeb Josephs (BIDVest Wits), Itumeleng Khune (Kaizer Chiefs)
Defenders: Vuyo Mere and Benson Mhlongo (Mamelodi Sundowns), Bevan Fransman (Moroka Swallows), Brett Evans and Bryce Moon (Ajax Cape Town), Tsepo Masilela (Maccabi Haifa/ISR), Nasief Morris (Panathinaikos/GRE), Aaron Mokoena (Blackburn/ENG, capt)
Midfielders: Lance Davids (Djurgardens/SWE), Kagisho Dikgacoi (Golden Arrows), Elrio van Heerden (Club Bruges/BEL), Teko Modise (Orlando Pirates), Surprise Moriri (Sundowns), Steven Pienaar (Everton/ENG), Siphiwe Tshabalala (Chiefs)
Forwards: Lerato Chabangu (Sundowns), Thembinkosi 'Terror' Fanteni (Ajax Cape Town), Katlego Mphela (SuperSport Utd), Excellent Walaza (Pirates), Sibusiso Zuma (Bielefeld/GER)