Melbourne Victory coach Tony Popovic has been left frustrated after his side conceded a pair of "soft" goals and had a late penalty shout turned down in a 2-1 A-League Men defeat to Newcastle.

Victory wasted a string of chances at McDonald Jones Stadium on Sunday as Roderick Miranda's clumsy tackle on Jaushua Sotirio led to Beka Mikeltadze's first-half opener from the penalty spot.

And while Victory winger Nishan Velupillay equalised after the break, Kosta Grozos punished the visitors' flat-footed defence at a set piece to net the Jets' decisive goal just before the hour mark.

There was controversy in stoppage time when Newcastle goalkeeper Jack Duncan went through the back of Victory's new signing Bruce Kamau in an aerial contest.

Kamau's head made first contact with the ball as Duncan attempted to punch it away.

The offside flag had gone up but replays showed no Victory players were offside when the cross came in.

There was no further action after VAR checks, leaving Popovic and Victory officials incensed.

"It was a game we should've won, no doubt, with the chances that we created," Popovic said.

"When we got back in the game at 1-1 we were in the ascendancy and we conceded a really soft goal.

"Poor organisation and they punished us, and then again you have to chase the game.

"We didn't get any lucky breaks there at the end with a few decisions but overall I think we made it hard for ourselves."

The result left Victory reamining last on the ladder, while Newcastle are unbeaten in five matches and knocking on the door of the top six after a second straight home win.

"We weren't where we wanted to be earlier on in the season and our performances have improved," Jets coach Arthur Papas said.

"There was a lot of grit in that performance as well.

"Some of the football was good, some of it was difficult at times, but I can't praise them (the players) enough for how hard they're working."

Grozos was initially named among the Jets' substitutes but was promoted to the starting line-up when Reno Piscopo suffered a groin injury during the warm-up.

The 22-year-old netted his first ALM goal - and Newcastle's winner - when he took a short pass from Mikeltadze's free kick, turned on the edge of the box and fired home in the 58th minute.

There was confusion amongst Victory players and they gave Grozos far too much space.

"I'm disappointed we lost (Piscopo) but Kosta came in and he scores the winning goal," Papas said.

"That's been coming for a while for Kosta, so I'm super proud of him."