In the masters men's 35-39 grade, Lonie (35) outclassed a strong field that included last year's runner-up, Chris Robb (Auckland).
Lonie pulled away from Robb and Auckland's Mike Waterman in the final stages to secure Otago's only gold medal at the national championships on the Waikanae Park course near Wellington.
The recent rain in the area had little effect on the course, allowing for firm underfoot conditions. Lonie completed the 8000m course in 28min 41sec, Robb clocked 29min 16sec, with Waterman third in 29min 34sec.
There was further success for Lonie when results in other grades set up a silver medal in the teams section for masters men 35-49.
Michael Wakelin finished second in the men's 40-44 behind reigning champion Richard Bennett (Canterbury), with Richard Hendry ninth in the same grade, and Ray Knox seventh in the masters men 45-49.
The Otago four earned 46 points to take silver behind Wellington on 37.
Despite some disappointing individual results, the Otago junior men's team won the bronze medal with Campbell Garry finishing seventh, Tony Payne 13th, Lyndon Brown 16th and Daniel Balchin 24th.
Otago's only other success came in the masters women's grade with Sue Cuthbert, a gold medallist in the women's 35-39 last year, winning bronze in the 40-44.
In the 45-49, Marion Maxwell and Maria Sleeman mirrored their results from last year with Maxwell winning silver and Sleeman finishing fourth.
Shireen Crumpton finished fourth in the senior women's event.
Ben Ruthe (Waikato) won the senior men's title in 39min 34sec.
