In a series of unfathomable decisions, Gillett booked four Phoenix players but none from Newcastle.
Ward was the most serious offender but his tackle on Ryan Griffiths 10 minutes from time deserved yellow not a straight red as he was not the last defender as Gillett meekly indicated.
Brown's second yellow for time wasting deep into stoppage time - and there was real doubt over his first - was laughable given the amount of time Gillett had, earlier in the game, allowed a Jets player to take a throw-in.
It was sad that such a poor refereeing display late in the game overshadowed a sterling effort from the home team.
Welcoming their team back for their first home game of the new Hyundai A-League season, the Yellow Fever had plenty to cheer about - especially the return to their very best form by All Whites Tony Lochhead and Leo Bertos.
Free of niggling injuries which hampered them for too much of last season, the duo were at their best when, on the hour, they combined superbly on the left before playing the ball in to Daniel Cortes, who stabbed home the match-sealing goal.
Earlier Brown had given the Phoenix their 20th minute lead when he ghosted between the Jets' central defenders to meet a pinpoint Ward cross to nod home a powerful header.
The visitors disappointed and rarely tested Tony Warner, who came in for Paston in the Phoenix goal.
By the end of the match the home side boasted a better than three-to-one superiority in both balls played into the opposition penalty area and in shots. The only concern was in not converting more of these chances.
Ben Sigmund and Andrew Durante again led the Phoenix defensive effort while Bertos, Cortes and Dani Sanchez provided the support for Chris Greenacre, who was left to shoulder the attacking responsibility in Ifill's absence.
All Whites midfielder Jeremy Brockie and most of his Jets teammates were largely anonymous as they showed few signs of a team who had started their campaign with a 3-2 home win over Melbourne Heart and the early league lead.
Their place in the top three is now deservedly taken by the Phoenix in another weekend sporting fixture clouded by red card controversy.
