The moves, confirmed by The Canadian Press, will be announced at a news conference Tuesday.
Earlier Monday, the worst club in MLS announced that technical manager Bob de Klerk has left by mutual agreement. With Mariner joining him on the way out, Toronto FC has wiped out the remaining ties to the Aron Winter era.
Mariner took over from Winter last June, becoming Toronto's seventh coach in six years.
The signing of Nelsen is a bold move by recently appointed Toronto president and GM Kevin Payne who has wasted little time tearing down the struggling MLS franchise since taking control on Nov. 28.
Nelsen, a 35-year-old New Zealander, played for Payne at D.C. United. This season, Nelsen has been one of the few bright spots at Queens Park Rangers in the English Premier League.
QPR manager Harry Redknapp confirmed recently that his defender had been offered a coaching job in North America.
"He has been fantastic," Redknapp told reporters. "I took him to Tottenham last year from Blackburn. He's one of the best pros I've ever met in my life, a fantastic player, a great trainer, a leader.
"He is a massive part of your team (but) he wants to be a manager and it is a chance for him to manage a club."
Nelsen is wasting little time leaving the pitch for the sidelines. He played 71 minutes for QPR on Saturday in a 1-1 draw with West Bromwich Albion in a third-round FA Cup match.
The Kiwi is undoubtedly a leader, having captained D.C. United, Blackburn Rovers and New Zealand.
A savvy, steady defender, he started his soccer career with Christchurch United in New Zealand before heading to the U.S. for stints at Greensboro College and Stanford University where he earned a bachelor's degree in political science.
Nelsen, then 24, signed with D.C. United in 2001 before moving to England in 2005 to join Blackburn Rovers, making more than 200 appearances for the Premier League club. He joined Tottenham last January, before moving on to QPR.
Nelsen has won 49 caps for New Zealand, captaining the All Whites at the 2010 World Cup and two Olympics.
If Mariner, who doubled as head coach and director of soccer operations, saw the writing on the wall when Payne was introduced as his new boss in Toronto, he hid it well.
"I think it's probably THE best signing that we'll make,'' Mariner said after watching the news conference introducing Payne from the front row.
At that news conference, Payne confirmed Mariner as head coach, noting he had a year left on his contract. But with the 5-21-8 club under construction once again, it seemed a short-term endorsement.
Change has been on the cards, with 10 players exiting the club in recent weeks.
Toronto started the season with nine straight league losses and Winter stepped down with the team mired at 1-9-0. The team rebounded under Mariner, going 4-2-4 in all competition before injuries and lack of depth took their toll.
The team finished with the season on a dismal 0-10-4 run in league play.
Winter, de Klerk and Mariner were installed as a threesome in January 2011.
As Winter's top assistant, de Klerk was fire to Winter's ice. He was a fervent advocate of the 4-3-3 system, relishing an attempt to demonstrate its advantages whenever a whiteboard was near.
And while he had a ready smile under his bald dome, he could also exhibit volcanic emotions. His raised voice was commonplace on the practice field.
With Toronto reeling from eight straight losses at the start of last season, the fiery Dutchman was shifted sideways in May when he was named technical manager. Jim Brennan, TFC's first signing and captain, moved up from the academy to become first assistant coach and Mariner, then the team's director of player development, was given more leeway to help coach the team's strikers.
The shuffle was clearly an attempt to address the team's woeful start without firing Winter as manager — although Winter insisted it was just a bid to better use his resources.
Some also suspected it was also a way to distance de Klerk from the first team. The previous game had seen de Klerk having to be separated from then Montreal manager Jesse Marsch after an altercation at the end of a 2-0 Toronto win at BMO Field.
No longer on the TFC sideline, de Klerk's new responsibilities included advance and international scouting, as well as serving as the "technical conduit" between the first team and academy program.
Winter said at the time the move would allow the team "to benefit more from his technical expertise and have him play a more active role in the day-to-day operations of the club off-the-pitch."
De Klerk worked with Winter at Ajax where he was a coach in the Dutch club's youth academy.
De Klerk spent nine years at Ajax and also worked with Ajax Cape Town of the South African league. Before moving into coaching, de Klerk played for KSV Waregem in Belgium and De Graafschap in the Netherlands.
Mariner was assisted by Brennan, Jason Bent and goalkeeping coach Stewart Kerr last season.Suggest a correction