The 22-year-old was born in Edinburgh but has not been involved in the Scotland set-up before now.
Jones plays for Cape Town-based Stormers in Super Rugby and his preferred position is centre.
He comes into Vern Cotter's 27-man squad after Glasgow Warriors fly-half Finn Russell pulled out after suffering a head injury.
Jones said: "I'm delighted to get this opportunity to play for Scotland. It's a dream come true.
"I didn't go out to South Africa with the intention of becoming a professional rugby player, but, as my career progressed, it become more of a realistic goal to play for Scotland.
"The call came as a bit of a surprise, but I'm thrilled and can't wait to get to Edinburgh next month and play my part in an exciting squad."
The Scotland newcomer was educated in Somerset, but his rugby career took off on a gap-year trip to South Africa in 2012.
He stayed on and helped the University of Cape Town win the Varsity Cup in 2014, scoring in the final, before being called up for Western Province Under-21s.
Jones progressed to the senior team before being called up by the Stormers, for whom he has made 21 appearances.
Scotland play two Tests against Japan on 18 and 25 June, with BBC Scotland providing live television, online and radio coverage.
Scotland have called up South Africa-based back Huw Jones for their June tour of Japan.