The Phoenix's failure to win their final game of the regular season means they will go into the elimination finals, with Melbourne City guaranteed to finish second.
Wellington dominated the first half but were unable to find a way past the Jets' debutant goalkeeper Noah James, and Nick Fitzgerald's deflected shot gave Newcastle the lead against the run of play on the stroke of half-time.
Stefan Marinovic made a couple of good saves before substitute Bernie Ibini drilled into the bottom-right corner following a swift Jets break in the 76th minute.
Wellington was unfortunate not to get a penalty when Callan Elliot went down under pressure from Connor O'Toole, and Newcastle had its second goal in three minutes when Jason Hoffman slammed Dimitri Petratos' backheel in off the underside of the bar.
The Jets consequently finish the season with a five-game unbeaten run, which included victories over each of the top three, while Ufuk Talay's Phoenix head into the Finals winless in four.