France-based Masibaka replaces Josh Bayliss, who suffered a groin injury while playing for Bath against Sale on Sunday. Bath head of rugby Johann van Graan described the injury as "serious".
Masibaka has impressed in the French second tier with Soyaux-Angouleme, where he is on loan from Montpellier.
The 23-year-old former Western Force player qualifies for Scotland through his Scottish-born mother.
Two locks - Cameron Henderson of Leicester and Ewan Johnson of Oyonnax - have also been called up alongside Glasgow's uncapped Euan Ferrie, who can play lock or in the back row, and Glasgow full-back Ollie Smith.
Captain Sione Tuipulotu was last week ruled out of the Six Nations after suffering a chest injury and Scotland are also missing Scott Cummings and Dylan Richardson.
Rory Darge and Finn Russell will be co-captains in Tuipulotu's absence as Scotland try to avenge last year's shock defeat by Italy in Rome.
