Driving her Citroen C3, she clocked a blistering time on the final attempt to beat two-time defending champion Jack Hawkeswood, of Hamilton.
Gilmour trailed her rival after the first leg but produced a flawless concluding sprint to finish 4sec clear.
The result reversed the fortunes of the past two years when she finished runner-up to Hawkeswood.
Mosgiel competitor Jake Thomas finished seventh overall in his Toyota Corolla to claim class B honours and the title of premier two-wheel-drive vehicle home.
Fellow southern motorist Ian Warren secured third in class B and 12th on the general leaderboard.
In class A, Oamaru racer Jak Elliott claimed success ahead of city rival Kevin Brockie.
Mosgiel entrant Richie Chadwick withdrew after experiencing engine issues during his initial pass.
Robbie Stokes, of Waikuku, also failed to finish the opening run in leg 1 when his Skoda Fabia went off the road.
Eastern Southland Car Club committee member Roger Laird said organisers were pleased for local star Gilmour.
‘‘We were absolutely delighted with the great entry and we thank the local residents for their co-operation as we run the event,’’ Mr Laird said.
‘‘We are thrilled for Emma [Gilmour], a member of our club, while disappointed Robbie Stokes had his day cut short.
‘‘We are rapt with the way the event went. It was a big ask with such a big entry list but a great team effort saw it go very well.’’
The Clinton competition involved two legs of roughly 9km on public roads, with final standings determined by combining the fastest times from both stages.
It served as the inaugural round of the Deep South Rallysprint Series.
