The interim coach was installed on a full-time basis on Wednesday, having acted in the role since Carl Robinson's sudden exit to Western Sydney Wanderers in December.
It was Deans' third temporary stint in charge of a club he first arrived at as a player in 2003, before serving as the Jets' Academy and W-League coach.
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Deans is contracted until the end of next season, the Jets opting for the long-standing club favourite over former Perth Glory coach Kenny Lowe, former Wanderers and Glory assistant Hayden Foxe and former Jets and Young Socceroos coach Gary van Egmond.
Deans thanked the fans and his support staff throughout the years for helping him secure the job.
"After successfully working through some challenging times as a club, we can now focus on moving forward and building a strong culture both on and off the field to enable us to bring success to this club and the Newcastle region," he said.
"I would like to thank Shane and the new ownership group for putting their faith in me and thank the players for their commitment and effort through the pre-season and the first seven games of the season. "
After four straight losses to begin the season, the Jets have won twice and drawn once to rise to eighth on the ladder.
"He comes from our community, deeply understands our club and our players, and has demonstrated his ability to deliver a very competitive team within a very tough competition," Jets chairman Shane Mattiske said.
"He is the right person for this team, this town and this region.
"Craig has created a side that is working for each other, working for him and working for our community and we look forward to seeing this momentum carry forward in this season's competition and beyond."