The two-time defending champions lost the dropped Test opener to concussion at the start of day two.
But with captain Ben Manenti closing in on his maiden first-class century, SA were firmly in the box seat.
They reached 6-352 on Thursday, a lead of 108 after bowling out Victoria for 244 late on day one.
Weatherald crashed into the boundary fence while chasing a ball in the field before lunch at Junction Oval on Wednesday.
He then faced only faced six balls at the end of day one before Victorian debutant Harry Hoekstra had him caught behind for a duck.
"Obviously he went a bit too hard into the wall. We thought he hit his neck, not his head, but he complained last night after play - he felt a bit sluggish, a bad headache," SA coach Ryan Harris said of Weatherald.
"He probably would have liked to have done it (concussion test) before he batted - he felt OK to bat, he said."
Matthew Gilkes was flown across on Thursday morning as the concussion sub. Harris was unsure if Weatherald would miss any games.
Weatherald was dropped from the Australian team in August after their shock first-Test loss to Bangladesh in Darwin.
Resuming at 1-4 on Thursday, SA built on opener Henry Hunt's 71 and 90 from No.6 Jake Lehmann to steadily take the initiative away from the home side.
Manenti and Noah McFadyen then combined for an unbeaten 89-run stand for the seventh wicket. Manenti will have a nervous night's sleep on 92, and McFadyen has made 46.
"I didn't expect to be 108 ahead - (I thought) if we could get to 60-70 ahead by the end of the day, it would have been good," Harris said.
"The partnerships were excellent and got us into a really strong position.
"It's a good wicket, so we're going to have to work out what we need."
After top-scoring with 45 for the home side, Hoekstra continued his excellent Shield debut with three more wickets and has led the Victorian attack with 4-57.
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