Mostert dominated the opening two races of the weekend, but a slight error in Race 3 saw him drop down to fifth position where he would ultimately finish. His efforts were still enough to win the round.
Off the track, Mostert edged closer to a personal sponsorship deal with Monster Energy drinks, displaying the company's logos on his car in Sunday's race.
Monster is keen to back a few young drivers in Australian motorsport, having upped its spend in local racing which includes backing reigning V8 Supercars Champion Jamie Whincup and New Zealand hero Greg Murphy.
Mostert, a former Australian karting champion, is working with Monster to lock in a deal soon.
In the meantime, Mostert extend his championship lead to 14 points over Nick Foster who finished slightly frustrating fourth for the round.
“What a great weekend for us, I'm just ecstatic to win here in Darwin and to break the stranglehold that Sonic has had on this circuit,” Mostert said.
“We had really good pace, which we didn't really expect. It was slightly disappointing to make an error on the oil in the last race, but that's racing.”
Pole-sitter Ryan Simpson struggled to match Mostert in the early races of the weekend, but came good in the final race to take the win from a recovering Ash Walsh.
“We've been missing something in the last couple of rounds in terms of balance and I think this weekend we really made some good steps towards a better package,” Simpson said.
“The balance improved all weekend and the car in the last race was probably the best it's been all season.”
Simpson's Sonic team-mate Geoff Uhrhane made a return to the podium in third, after two tough rounds plagued by mechanical problems. The Hog's Breath Café driver challenged Mostert early in the weekend and finished third in the final race to secure his spot on the podium.
“It feels great to be back on the podium, but we'd like to be a little further up,” said Uhrhane.
“It was an interesting weekend of racing, but things just didn't go our way in the final race.”
Race 3 saw a long safety car period triggered by an incident involving Ben Jurczak and Nathan Morcom that resulted in Morcom's car flipping over. Both drivers emerged from the incident uninjured.
Round 5 of the Genuine Ford Parts Australian Formula Ford Championship will take place at the Townsville Street Circuit in far north Queensland on July 9-11.