Howard, who can play on the wing or in the centre, joined Saints from Western Province in April 2015.
The 24-year-old played for the Stormers in Super Rugby and also had a spell with Munster last season.
"I am really looking forward to returning to play in the Pro12," said Howard, who won the Junior World Championship with South Africa in 2012.
"I am sure that there are good times ahead with a young and exciting squad being assembled and I am looking forward to making the move to Wales."
Dragons head coach Kingsley Jones said the region had been monitoring Howard's progress for 18 months.
"He is a dangerous attacking player with both strength and pace, and his physical nature of playing will add to our youthful backline," Jones said.
Northampton's South African utility back Pat Howard will join Newport Gwent Dragons for the 2016-17 season.