Cricket Australia hastily booked Marsh on a flight to Johannesburg on Saturday night (AEDT), when Watson was unable to run at full pace due to a calf injury.
Marsh was in Australia's original 15-man touring party for the three-Test series, but his own calf issue meant Phillip Hughes boarded the plane instead last week.
While Watson made limited progress after tweaking the muscle at training in Potchefstroom last week, Marsh's calf mended faster than first expected.
The 30-year-old made a surprise return in the Big Bash League final, belting an unbeaten 63 to lift the Perth Scorchers to a 39-run win.
He will now battle Alex Doolan for the right to bat at first drop at Centurion in Watson's absence.
Watson's latest injury concern is so restrictive he would not even have been capable of playing on Wednesday as a batsman.
The squad has only three days off between day five of the first Test in Centurion and the start of the second clash in Port Elizabeth.
"I think he's a good chance to play (in the second Test), but we need to see what he gets from this (setback)," Australia physio Alex Kountouris said.
"Hopefully he gets to the point where he's able to train unrestricted by two or three days' out (from the Test), which is what we were planning to do here.
"He's had these before ... they can take a short period of time or they can take an extended period of time. In this case it's looking like it's going to be a little bit longer.
"Our first priority is to try and get him back as a batter, give the selectors that option (of playing him as a batsman)."
Earlier this week both coach Darren Lehmann and team doctor Peter Brukner insisted Watson would bowl before the first Test and be fine to play.
The 32-year-old played all 10 matches in the back-to-back Ashes series, overcoming hamstring and groin niggles to take part in the Brisbane and Sydney Tests respectively.
Kountouris noted Watson was very disappointed to be missing his first Test since returning home from India amidst 'homework-gate'.
"As we all are. We were very happy we got everyone through the past Ashes," he said.