The former Perth Glory mentor - the Roar's fourth coach this season - has been interim boss for the past 11 games, recording three A-League Men wins, four draws and four losses.
The eighth-placed Roar, who finish their season at home against Adelaide on Friday, can't make finals.
But the former Socceroo's efforts to steady the ship after newly-installed coach Ross Aloisi's sudden exit late last year have earned him an extended stay.
Assistant Luciano Trani lasted just one game in the top job before his replacement Ben Cahn - the team's fifth coach since February - took sick leave and then resigned last week.
"I am also very excited to embrace the opportunity to lead the club through the challenges ahead, with a dedicated staff line-up, an extremely loyal fan base and a very committed group of players that can take the club upwards again," Zadkovich said.
"In challenging circumstances this season, we have been supported by a strong membership base and match attendances, confirming just how loyal and passionate the Brisbane Roar fans are for their team and club."
"I'm excited to be planning for next season in many facets of the club and football department.
"We're aiming to reward those loyal fans and members with the sort of attacking, dynamic football that encapsulates the Queensland spirit and football DNA that has brought the club success in the past."
Chief executive Kaz Patafta has overseen frequent change since taking over last July.
"Ruben is one of a new wave of young Australian coaches who have made the A-League so exciting in recent seasons, and we're delighted he's committed to us for the next two seasons," he said.
"We feel we have a lot of young talent at this club and Ruben is the ideal figure and leader to help our men's team develop into another of the great Brisbane Roar teams.Â
"We have already begun planning what our senior squad will look like for next season with the aim of displaying a really positive brand of football."
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