Santos have requested that Rodgers return to Cape Town to help them in the Promotion/Relegation Play-offs, which were suspended but resume this weekend. Santos face Chippa United on Wednesday, June 20.
"I think I am missing out on a wonderful opportunity to play for my country, but then again my club also needs me," the striker says.
"It's the kind of situation no player wants to find himself in, but like I have been saying everything happens for a reason. I just hope I get another chance to play for Bafana Bafana and show what I can give to the nation.
"It's really sad but I have to take it the way it is. I also want to wish Bafana Bafana the best of luck against Gabon, hope they do really well."
Rodgers, who did not take part in the squad's last training session at Mbombela Stadium, will depart for Cape Town on Friday morning.
Caretaker coach Steve Komphela says the situation is regretable but understandable.
"This is out of my hands, but if you ask me I would have loved for the boy to stay and play for his country. We had worked so much with him at training and just on the eve of the match we get news that he has to return to his club.
"It's a sad situation for the player and for the team, but we have to soldier on and find an alternative approach to the match."
Komphela now has 20 players to choose from for the clash, after releasing five players from the squad earlier in the week.
After two draws in the World Cup qualifiers, South Africa now face a Gabon side ranked 49th in the world, compared to Bafana Bafana's 69th.
"We are optimistic that we will do well, whoever starts knows what they must do and what is expected of them," Komphela says.
"The team has been formulated and we need the confidence and the inspiration not only for ourselves but also for the nation. It is bad when South Africans get into the mode of saying 'I hope we win,' but we need to say a win is guaranteed irrespective of where Gabon is placed in the rankings."
Meanwhile tickets for the match are still available.
Tickets on the lower and upper concourse are R50 and can be bought at Computicket outlets, Shoprite and Shoprite stores around the country.
No tickets will be sold at the stadium on match day.
Park and Ride: There will be a full park and ride in operation for the match on Friday, June 15, at the following pick-up points: Riverside Mall Public Transport Hub in the CBD Show grounds
• All match tickets entitle spectators to use the buses
• Spectators must present a valid match ticket when boarding the buses to the stadium
• There will be two pick-up points at the stadium after the match that will be clearly marked
• The same buses will be travelling to Public Transport Hub and the Show Grounds after the match
• Buses will transport spectators to the pick-up points until all spectators have left the stadium and there will be no need to rush for the buses
• There will be sufficient buses to transport all the spectators
• Buses will start leaving the pick-up points at 5pm. Kick-off is 8.30pm.