The Manchester United player could still face Denmark on Monday, although Scotland will hope they have secured the three points they need to be guaranteed a play-off place after the game in Chisinau on Friday.
Speaking from the team's training camp in Alicante, manager Steve Clarke said: "Almost everyone is good. Unfortunately, Scott McTominay has picked up a bit of a throat virus so we have sent Scott home to rest and recuperate and hopefully he will join us again at the weekend."
McTominay played both in defence and midfield as Scotland beat Israel and the Faroe Islands last month to keep their play-off destiny in their own hands.
Clarke said: "I looked at the squad and obviously you can think about calling someone up but we have good cover at centre-back and good cover in midfield.
"Yes it's disappointing to lose Scott, but it's going to be a big chance for someone else to play in the team."
McTominay's absence means Clarke will have to make at least five changes from the team that beat the Faroe Islands thanks to a late goal from Lyndon Dykes, his fourth in as many internationals.
Forwards Dykes and Ryan Christie are suspended, while centre-back Grant Hanley and Ryan Fraser withdrew from the squad.
Clarke called up John Souttar on Sunday and the Hearts defender now has a real chance of starting, while Stoke forward Jacob Brown could win his first cap in Moldova.
When asked whether Brown was ready after his first few days of training, the Scotland boss said: "Anybody that I have picked for this squad is a player that can contribute. Anybody in this squad can contribute whether it's from the start or off the bench.
"Yes it's disappointing to lose Lyndon because he was on a good scoring run for us, but what a great chance for someone else to be the guy that catches the headlines on Friday night. It's a big chance for someone else."
With Kieran Tierney confirmed as 100 per cent fit following an ankle problem, Clarke's other options in a likely back three are Jack Hendry, Souttar and Liam Cooper.
Che Adams is almost certain to start up front with Kevin Nisbet also vying for a place, and the likes of John McGinn, Stuart Armstrong and David Turnbull could be utilised in an advanced midfield role.