20th June, India v South Africa, 09:30 GMT
Flynn missed the second Test with a hand injury and could come straight back into the side after his replacement Jamie How failed to make an impression while Southee has been called up on the back of some good form for Northern Districts.
"Tim's inclusion gives us additional options with the new ball, and strengthens the attack against this strong Indian batting lineup," chief selector Glenn Turner commented.
Fringe players Brent Arnel and Jacob Oram were not considered due to injury while Flynn's fitness will be assessed ahead of the match at the Basin Reserve.
India lead the series 1-0 after a ten-wicket win in the opening match in Hamilton.
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