The British and Irish Lions back had been a doubt for the clash at Kingsholm having picked up a problem during the Scots' last warm-up match, and was seen sporting a protective boot in the weeks after the game.
Hogg's availability means Vern Cotter is able to name a near full-strength side, with scrum-half Greig Laidlaw set to captain the team.
Mark Bennett and Matt Scott are named in the centres, while Sean Lamont will earn his 98th cap for Scotland having been given the nod to start on the wing.
Grant Gilchrist will partner Jonny Gray in the second row while flanker Josh Strauss has been handed a place amongst the replacements having become eligible under the residency rule last week.
Cotter admits he selected a strong side after watching Japan cause a huge upset when they beat South Africa at the weekend and says his players will not be underestimating the Brave Blossoms.
"We've prepared well for what will be a very tough Test against a powerful and fit Japanese team, who like to play a high-tempo game," he said.
"They will have taken a lot of confidence from their opening win over South Africa. However, that doesn't change our approach to this game or the pool.
"The priority for us to ensure that we get our jobs right with accuracy, and impose ourselves on the game."