AB de Villiers will lead South Africa in the last two matches after Hashim Amla announced his shock resignation as test captain on Wednesday, minutes after the drawn second test at Newlands.
"I don't think it will make much of a difference to the South African team, they have an able replacement," Bayliss said.
"Obviously Amla will still be in the team and he is in form. He scored 200 runs and it might free his mind up even more," said the Australian.
"AB is a guy with a lot of experience and has done the job before. I can't see too much of a problem there," Bayliss said.
Amla's captaincy and form were under scrutiny after the team's humbling 3-0 defeat on their tour of India last month.
Amla said he was quitting because he wanted to focus on his batting and that there were better candidates to lead the team.
His decision came just when he seemed to be getting right the balance between captaincy and batting form. The right-hander hit 201 at Newlands to rescue South Africa from going 2-0 down in the series.
England are 1-0 up in the four-match series, which resumes with the third test in Johannesburg from Thursday.
(Editing by Amlan Chakraborty)
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