The 35-year-old central defender was given his new job on 8 January and QPR fans have been waiting to hear when he will depart for Canada.
The New Zealand international, who moved to west London from Tottenham last summer, will make his final appearance for the Premier League's bottom side at home to Manchester City next Tuesday.
The news is a blow to QPR's hopes of retaining their Premier League status, with Nelsen having been one of their outstanding performers this season.
Upon learning Nelsen was to depart at some stage, QPR boss Harry Redknapp said: "The longer he's here, the better for us, because he's a fantastic player, a great person and a top professional.
"We need him around as long as we possibly can, so hopefully we can keep him for most of the season."
But after Saturday's 1-1 draw at West Ham, Redknapp said: "We're going to lose him unfortunately."
Toronto FC have never reached the Major League Soccer play-offs and finished with a franchise-worst 5-21-8 record last season.
They have already begun their pre-season training camp and their 2013 season kicks off at Vancouver on 2 March.
Wearing a Toronto tracksuit top, he said of his change in roles: "I just love it. It's where my head's been for a few years now. You love everything about football but playing I didn't really enjoy so much as coaching. When that was happening, I knew it was time."