Hearts captain Shankland, 30, has scored 10 goals this season and has helped the Jambos to the top of the William Hill Premiership where they have a nine-point lead over Celtic having played a game more.
The Gorgie striker last featured for Scotland in the Nations League victory over Poland 12 months ago.
Falkirk goalkeeper Bain, 33, won the last of his three caps in a 2-0 win away to San Marino in March 2019.
Bristol City utility player Ross McCrorie and Sassuolo defender Josh Doig are also included in the group as Nottingham Forest goalkeeper Angus Gunn and Hibernian striker Kieron Bowie drop out.
The Scots have 10 points from four Group C fixtures and will guarantee a final-game decider against the Danes if they can get at least a point in Piraeus on November 15.
Scotland, however, have at least a play-off spot in March in the bag.
Scotland captain Andy Robertson won his 88th cap against Belarus last month and could win his 90th cap, should he feature in both matches.
Vice-captain John McGinn moved level with goalkeeper Craig Gordon on 81 caps last month, overtaking Darren Fletcher in the process to move joint-fifth in the all-time cap list.
Scotland have not reached the finals of the World Cup since France 1998.