Manly mentor Geoff Toovey's right hand man Brad Arthur had firmed as favourite to receive the nod from North Queensland after master coach Wayne Bennett ruled himself out of the running.
But it was the team the Sea Eagles hope to topple in Sunday night's decider - the Sydney Roosters - that will provide Neil Henry's successor at the Cowboys.
Green - who is also the Roosters under 20s mentor - was officially confirmed as the first ex-Cowboys player to return to the NRL club as head coach by North Queensland after reports linked him to the job on Tuesday morning.
Green suddenly became the favourite after reports emerged on Tuesday Arthur had been told by the Cowboys that he had missed out on the job.
Broncos legend Kevin Walters and Brisbane assistant Kristian Woolf had also applied.
"We undertook a very thorough process with filling our coaching vacancy and Paul proved to be the outstanding candidate in a very high-quality field," Cowboys CEO Peter Jourdain said.
"We strongly believe he is the right person to take our club to the next level of performance and our ultimate goal - winning our first premiership."
Green's appointment provided another twist in the rollercoaster end to the Cowboys' 2013 season.
He replaces Henry who was told in July his services would not be required in 2014, sparking a remarkable six-game winning run that propelled North Queensland into an unlikely finals campaign derailed by Cronulla's infamous seventh tackle try.
And there was another unexpected turn when Bennett was linked with the Cowboys after he cryptically claimed there were "no guarantees in rugby league" when asked about his future following Newcastle's 40-14 finals loss last weekend.
Green had enjoyed assistant roles at Brisbane and the Roosters but has never held an NRL head coach job, unlike Arthur who was interim Parramatta mentor last year.
But Jourdain said the knowledge gained from Bennett at the Broncos along with his stint under Trent Robinson who has steered the Roosters to the grand final on debut had got Green over the line.
Green will start work with the team he played 35 games for from 1999-2000 during a stellar 10-year NRL career when North Queensland begins pre-season training in early November.
"I've always wanted to be a head coach in the NRL and now I have that chance with an outstanding football club that already has a high-quality playing roster in place," Green said.