The Manchester United midfielder needed groin surgery last month which forced him to miss the wins against Moldova and Austria.
He returned for United's 2-1 win at West Ham and also started Saturday's 1-0 defeat to Aston Villa.
Southampton's Stuart Armstrong is also in the squad having pulled out through injury ahead of September's 2-0 loss to Denmark.
Rangers goalkeeper Jon McLaughlin replaces Zander Clark in Steve Clarke's squad and Callum McGregor is also included despite missing Celtic's last four games through injury. Club team-mates James Forrest and Greg Taylor miss out due to injury.
Scotland are second in Group F, four points clear of Austria and one point above next opponents Israel with the play-off spot in their own hands.
They host Israel on October 9 and visit the Faroes three days later.
Scotland squad: Gordon (Hearts), Kelly (Motherwell), McLaughlin (Rangers), Cooper (Leeds United), Hanley (Norwich), Hendry (Club Brugge), McKenna (Nottingham Forest), O'Donnell (Motherwell), Patterson (Rangers), Robertson (Liverpool), Tierney (Arsenal), Armstrong (Southampton), Ferguson (Aberdeen), Gilmour (Norwich on loan from Chelsea), McGinn (Aston Villa), McGregor (Celtic), McLean (Norwich), McTominay (Manchester United), Turnbull (Celtic), Adams (Southampton), Christie (Bournemouth), Dykes (QPR), Fraser (Newcastle), Nisbet (Hibernian).