Coneo's run of 16:38 was six seconds slower than his winning time last year but was enough to propel the Vikings to their first team title in six years.
Meanwhile, Trigg County's Jay Jolly finished in 11th place, covering the 3.1-mile course in 18:50. Zeke Wright was 30th in 19:54, and Grady Cofield was 56th in 22:19.
Coneo is the first runner since Calloway County's Shawn Covington in 2001-02 to repeat as male individual champion. As a team, Northwest edged Kenwood 91-97, while Fort Campbell was third with 122 points. Trigg County did not field a complete team.
In the girls' race, Graves County's Elizabeth Beach won the race in 20:51, becoming the first Graves female runner to win the varsity race. Last year's winner, Meagan Summers of Calloway County, finished ninth.
Beach helped Graves County win their fourth straight team title with 28 points. Fort Campbell (69) finished second, and Clarksville Northwest (97) was third.
Rachel Cronin finished 45th for Trigg County in a time of 29:31.
In the middle school boys' race, Romaine Cunningham led the Midcat runners across the finish line in seventh place in a time of 15:54 over the 2.4-mile course.
Jakelzie Martin finished 11th in 16:17, followed by Jayven Jones (35th, 18:35), Corbin Estes (36th, 19:07), Landen Sumner (37th, 19:20), Alex Peacock (46th, 20:12), Duncan Mangles (58th, 22:26), Matthew Brokering (60th, 23:43), and Hunter Allen (61st, 24:00).
Calloway County's Ryan Thurmond won the race in a time of 14:21.
St. Mary won the team title with 41 points. Graves County was second with 75 points, followed by Trigg County (126), Murray (128), Calloway County (129), Christian County (147), and Fulton City was seventh with 150 points.
In the middle school girls' race, Graves County's Kelly Beach won with a time 16:58, helping the Lady Eagles to the team title with 44 points.
Shakandace Malone led the Trigg County runners with a fifth place finish in a time of 17:50. Macey King was 14th in a time of 18:35, followed by Alex Olin (15th, 18:52), Lanese Byars (20th, 19:23), X'zashea Mayes (39th, 21:59), and Benna Matlock (47th, 23:06).
St. Mary finished second behind Graves County with 50 points, while Trigg County was third with 93 points.
There were 16 schools and 243 runners represented at the race, which saw some brief rain during the girls' varsity race.