The London, Ont., native finished first with 8,145 points, well ahead of Ottawa's Patrick Arbour who was in second with 7,252.
Warner was fifth at last summer's London Games and recently won the prestigious Hypo Meeting in Austria — the unofficial world championships for multi-events.
Warner's victory also booked him a ticket to the world championships being held in Moscow in August.
In the men's 3,000-metre steeplechase, Matt Hughes, Chris Winter and Alex Genest each secured spots at the world championships.
Hughes, from Oshawa, Ont., finished first ahead of Vancouver's Winter and Genest of Lac-aux-Sables, Que.
Three spots were up for selection to the team bound for Moscow. Taylor Milne of North Bay, Ont., who had the A standard but needed a top-three result to qualify, fell on the final water barrier and finished fifth.
Tim Nedow of Brockville, Ont., won his first shot put championship with a throw of 20.72 metres. He was followed by Kamloops, B.C., natives Dylan Armstrong (20.31) and Justin Rodhe (19.61). All three also qualified for the world championships.
Julie Labonte of Sainte-Justine, Que., won the women's shot put title with a toss of 17.61 metres.