"The sentence imposed... in respect of murder is set aside and substituted with the following: the respondent is sentenced to imprisonment for a period of 13 years and five months", the judge said, reading out the court's decision.
Johnson said the High Court did not list the substantial and compelling factors for deviating from the 15-year sentence and that Pistorius had not shown remorse for the murder.
In July 2016, South Africa's National Prosecuting Agency deemed the sentence "shockingly too lenient", announcing plans to appeal for a longer sentence.
Prosecutors had called that six-year sentence "shockingly" lenient. He will now serve the 15-year minimum for murder in South Africa.
Tania Koen, a spokeswoman for the Steenkamp family, said: "This is an emotional thing for them".
Pistorius, 31, was convicted of killing his girlfriend, Reeva Steenkamp, with a gun in his home in Pretoria in February 2013.
Pistorius has said that he thought an intruder had broken into his home and he shot Steenkamp by mistake.More news: United States authorities identify alleged Game of Thrones hacker
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The Supreme Court said that Pistorius "displays a lack of remorse, and does not appreciate the gravity of his actions".
Supreme Court judges are generally reluctant to change sentences handed down by trial courts, and it's rare for them to change one so dramatically.
Pistorius must serve at least half of the 13 years and five months - almost seven years - before he can be considered for parole.
The matter has been subject to a protracted legal battle for over four years and even the athlete's initial homicide conviction did not bring closure.
Pistorius' lawyers have one avenue left open to them if they want to challenge the new sentence, and that is to appeal to the Constitutional Court, the highest court in South Africa.
At the same time, Steenkamp's parents have sent their love to Jayde Panayiatou's parents after her husband, Chris, was sentenced to life in prison for her murder. The court agreed and the sentence is now 13 years.