The deal will keep the 22-year-old at the Saints until the end of 2020.
Originally drafted with pick No. 41 in the 2014 AFL Draft, Lonie has played 50 games for the Saints and kicked 44 goals.
The small forward managed 16 goals in 11 games in 2018, with 11 of his majors coming in the last five rounds of the season.
Lonie told the club website he is looking forward to being part of the Saints future success.
“I’m really excited to have signed on for a further two years,” Lonie told the Saints website.
“I really believe in what we’re doing here at the Saints and that this group is capable of some real success, and I’m looking forward to being part of it.”