Groombridge, 26, had finished runner-up to Macdonald, 19, at the opening round, south of Nelson in mid-February, and he backed that up by finishing third at round two near Whangamata a week later, while Macdonald finished runner-up at Whangamata, giving the South Islander a slender five-point outright lead after two rounds.
However, with Groombridge a non-finisher on Saturday, while Macdonald finished third overall, it means Macdonald's championship lead has ballooned out to 17 points over the new No 2 rider in the series, Mokau's Adrian Smith.
"About three stages into the day I knew that Brad [Groombridge] was out," said Macdonald. "That news lifted a lot of weight off my shoulders, but I was still pushing for the win.
"I know now that, if I ride sensibly at the remaining rounds, the title should be mine, but anything could still happen."
Macdonald's younger brother, Hamish, won the day at Moonshine, finishing just 34 seconds ahead of Smith, with Angus Macdonald and Cambridge pair Dylan Yearbury and Simon Lansdaal rounding out the top five.
Helensville's Tom Buxton had his worst result of the series thus far, finishing the day eighth overall at Moonshine, but he remains third overall in the series standings.
Titirangi's Callan May suffered engine failure in the final section of the day and, despite his impressive performances earlier in the day, it dropped him to 23rd in the expert grade and from fourth to 10th in the overall championship standings.
One of the big movers on Saturday was Hamish Macdonald. He had been 10th overall in the standings at the start of the day, but his impressive win at the weekend has elevated him up to fifth overall after three of six rounds.
Meanwhile, it's a battle of the ages in the fight for intermediate grade honours.
The leading intermediate grade riders after round three are 16-year-old Whitianga rider Blake Wilkins, 54-year-old Ellerslie rider Jeff Van Hout and 53-year-old Helensville man John Buxton.
Round four will be held near Christchurch on May 6 and then Waitawhiti Station, east of Eketahuna, hosts round five on June 3. Finally, the enduro nationals wrap up near Tokoroa just two days later, on June 5.