Watson, 56, will work alongside Mark McGhee as assistant to Scotland manager Gordon Strachan.
McCall left his role with Scotland after more than three years to take over as manager of Bradford City.
"It is an honour and a privilege to have been asked to help my country and, it goes without saying, I had no hesitation in doing so," said Watson.
It is a second spell as part of the of the coaching set-up for the former Birmingham City, Hibernian, Motherwell and Rangers coach, having worked under Alex McLeish during the Euro 2008 qualifying campaign.
Watson knows his new colleagues well, having played alongside Strachan and McGhee at Aberdeen in the late 1970s and early 1980s.
He added: "I actually missed Gordon's call when he phoned and, when I called him back, I thought it would be to organise scouting, so I was humbled when he asked if I would be willing to help out for the World Cup qualifiers.
"It was a great experience to work with the national team set-up before, under Alex, and we came really close to qualifying then.
"I am confident that we can go a step closer this time and I am really excited about getting started and helping Gordon and Mark in any way I can."

Reports in France suggest Toulon coach Diego Dominguez's job is under threat, and Lancaster, 46, is viewed as a potential successor.
He left his role with England after their exit from the 2015 World Cup.
Since his departure, Lancaster has been an adviser to the Football Association, the NFL and British Cycling.
He is interested in the Toulon job, but is understood to still be keen on a role in the southern hemisphere, with posts in Australia at the Queensland Reds and the Western Force both available.

Samantha Ho, 39, was found in Curlew Place, St Neots, Cambridgeshire, on Saturday.
Her husband Timothy Allen, 40, is due to go on trial in Cambridge for her murder next year. It was previously reported Mr Allen was Ms Ho's partner.
Mr Allen was due to appear via video link at the Old Bailey, but it was decided he did not have to attend.
His first Crown Court hearing went ahead in his absence.
Judge Mark Lucraft QC set a provisional plea and case management hearing for 13 November at the Old Bailey.
He said the trial at Cambridge Crown Court should be before a high court judge.
A provisional two-week trial has been set to start on 22 February.
No application for bail was made.
Andy Watson has been brought into the Scotland coaching set-up to replace Stuart McCall.
[NEXT_CONCEPT]
Former England boss Stuart Lancaster is meeting Toulon president Mourad Boudjellal this week as he seeks a return to full-time coaching.
[NEXT_CONCEPT]
The man accused of beheading a scientist was her husband, it has emerged.