Johnson is one of 10 changes made by head coach Gregor Townsend from the side that defeated France last weekend.
Rory Hutchinson makes his first Test start for Scotland in Tbilisi on Saturday and hooker Stuart McInally returns to captain the side.
Blair Kinghorn, Allan Dell and Matt Fagerson also feature in the XV.
Wing Darcy Graham replaces the injured Tommy Seymour, with Sean Maitland remaining on the other flank of the back-three. Returning half-backs Greig Laidlaw and Finn Russell complete the back division.
Prop Willem Nel starts again on the tight-head side alongside Dell and McInally in the front-row, while second and back-row forwards Grant Gilchrist and John Barclay have been promoted from the bench.
Townsend said: "We're pleased to welcome Sam (Johnson) back into the side, having performed so well for us in the spring, while a number of other players also get the opportunity to build on Saturday's performance.
"There were improvements in our back-to-back games against France, in particular in defence, game management and at scrum, as well some elements of our attack."
1 Allan Dell (London Irish)
2 Stuart McInally CAPTAIN (Edinburgh)
3 Willem Nel (Edinburgh)
4 Ben Toolis (Edinburgh)
5 Grant Gilchrist (Edinburgh)
6 John Barclay (Edinburgh)
7 Hamish Watson (Edinburgh)
8 Matt Fagerson (Glasgow Warriors)
16 Grant Stewart (Glasgow Warriors)
17 Jamie Bhatti (Edinburgh)
18 Zander Fagerson (Glasgow Warriors)
19 Scott Cummings (Glasgow Warriors)
20 Josh Strauss (Blue Bulls)
21 Ali Price (Glasgow Warriors)
22 Adam Hastings (Glasgow Warriors)
23 Huw Jones (Glasgow Warriors)