Thompson, who last held the Otago half-marathon title in 2006-07 after winning on the Hill Free course at Outram, was pulled through the first 10km at a shade over a 3min pace by Peninsula Challenge champion Neal McLanachan.
When McLanachan succumbed to the pace shortly after the halfway mark, Thompson was forced to continue alone up front, breaking the tape in 1hr 11min 56sec, well clear of Jonah Smith (1hr 15min 57sec) and Glen Chisholm (1hr 17min 6sec).
The decision to enter the Balclutha event only came about when Thompson (34), a Dunedin physiotherapist, realised he would not be able to contest the Edmond Cup steeplechase on July 12.
''I needed a race under my belt before the Otago cross-country,'' Thompson said, looking towards the July 26 title race.
''The winter racing calendar is a bit sparse compared to summer, and this proved a good little hit out.''
Thompson has been in top form this year, with impressive off-road victories in the Three Peaks in April, preceded by victories in the Motutapu marathon (2hr 56min) and Hanmer mountain marathon (2hr 39min).
His wife, Bridget Thompson, finished second to Dunedin's Mel Aitken in the open women's section in 1hr 29min 11sec.
Aitken's run, in 1hr 24min 32sec, was impressive, coming hot on the heels of back-to-back sub-3hr marathons in the past three months.
It also sealed a rare double for the runner, who has won the Otago marathon title the last two years.
Aitken appears in ominous form in search of a third straight Otago marathon title on the Dunedin course in September.
She clocked 2hr 59min 31sec to finish seventh in the open women's section on the Rotorua course in April, and 2hr 56min 55sec to finish third in the Christchurch marathon at Queen's Birthday Weekend.
Third in the open women's section in Balclutha was international ironman representative Tamsyn Hayes in 1hr 31min 13sec.
In the associated 10km event, Otago middle-distance champion Joe Beamish won the open men's title in 35min 43sec, and Louisa Andrew won the open women's in 39min 16sec.
Hanna English (Columba College) won the senior girls national secondary schools cross-country championship title in Palmerston North on Saturday.
The Dave Stinson-coached athlete dominated the field over 4km to win comfortably in 16min 5sec, from the Auckland pair of Audrey Gregan (St Cuthbert's College, 16min 10sec) and Isabella Richards (St Kentigern College, 16min 22sec).
