Greencastle lost runner Elijah Brattain before the race due to illness and South Putnam capitalized on a strong back end to claim the boy's county title by three points, 29-32.
North Putnam finished third with 87 points, followed by Cloverdale, with a score of 95.
Eagle junior Hunter Barr managed to hold off a furious charge from Tiger Cubs senior Tyler Hudson to claim the overall race title in 17:21.72, while Berndt Freeman of South Putnam finished third.
Taylor Secrest placed fourth overall for Greencastle, while North Putnam's Dalton Spear placed fifth.
Nick Blundell was the highest finisher for Cloverdale in 13th place.
South Putnam's ticket to victory, however, was in the finish of Lane Franklin, Matt Lund and Matt Allen.
Franklin finished seventh, followed by Lund in eighth. Allen finished 10th to seal the win for the hosts.
Greencastle's Jacob Lewis finished sixth, Matt White finished eighth and Levi Lewis finished 11th, but the runs were not quite enough to save the Tiger Cubs from losing hold of the county title.
South Putnam head coach Brandon Welti was excited for the win but wanted to see it happen with Greencastle at 100 percent.
"Obviously the guys are excited about winning, but knowing Greencastle wasn't at full strength kind of takes a little bit of the victory away," Welti said.
"Nonetheless, the team that shows up healthiest on the day of the race counts and our boys did that. They put in a lot of time this year and they earned it. They did a great job."
Welti said that Hunter Barr's win was a big boost for the rest of the squad, though Barr was nearly overtaken by Greencastle's Tyler Hudson.
"Hunter told me that he was cruising along and forgot about the kind of turnover that Hudson had and it caught him off guard," Welti said.
"But I'm glad he was able to respond and hold him off because that might have hurt us in the race for the title."
Even after winning the county title, Welti said that his squad would be looking up at stiff competition at Saturday's WCC meet.
"We know that despite the results today, if Greencastle and Cascade are healthy, we're the underdog in the race," Welti said.
"If both squads are healthy, they have probably the best chance of winning, so we need to keep moving up as we've been doing lately.
"If our three, four and five keep improving like they have been, we're right in that mix as well and we have a shot to win."
Greencastle boys' coach Art Dwigans said that keeping Brattain out was precautionary, but that the rest of the squad stepped up in a big way.
"I think the boys ran pretty well. We went without Elijah today and Tyler was running his first race in three weeks," Dwigans said.
"I thought they all ran hard but just came up three points short. I think you could race this race 10 different times and come up with ten different results.
"The rest of the guys picked up the slack a lot better than they had all year in trying to pick up for Elijah. I felt our three through six runners came in strong," Dwigans added.
Greencastle will defend the WCC title on Saturday and Dwigans said that the squad now knows what kind of challenge to expect.
"A lot of the thinking in holding Elijah out was looking ahead at Saturday's race. Elijah could have raced today but he would have only been at 50 percent and we'd rather have him at 100 percent Saturday," Dwigans said.
"We're still coming here to in on Saturday. The boys know that they have some work to do and know who they need to race now. I think we can get a better result on Saturday."
North Putnam head coach Kevin Lutes noted the run of Dalton Spear in pacing the Cougars to third place.
"Dalton did a great job. He's done a better job this year of running smarter than what he had been. He was in the thick of things early but fell off a bit," Lutes said.
"I think he recovered well and had a good time. The boys altogether pulled out third, so I was really happy with that. A lot of them were really keyed up going into the race and they ran well."
Lutes added that the squad needed to bear down and focus on their own races Saturday.
"We just need to go out and run our own race. The hardest thing we fight with is trying to keep people from going out faster than what they should be," Lutes said.
"If they start out too fast, they'll be shot for the rest of the race so if they can rein it in during the first mile, the things we've been doing the rest of the year will kick in and we'll be alright."
Cloverdale head coach Kyle Walter said that the boys ran hard and needed to do so again on Saturday.
"The guys ran hard, but we didn't place as high as I had hoped for today. Our plans for Saturday are the same as today. Hopefully, now that we've seen the course again, we'd like to get a better result on Saturday."
In the middle school race, Greencastle took five of the top six spots to win the meet with 17 points over second place South Putnam on 45 and Cloverdale on 85. North Putnam did not have a team score.
Ben Gellman won the race for the Tiger Cubs, finishing six seconds ahead of second place Clayton Wilson with a time of 12:23.01.
Jacob Crawley finished third, followed by South Putnam's Blake Clearwaters. Jace Featherson placed fifth and Jackson Kendall placed sixth to round out the Greencastle scoring. Tylan Jones finished seventh to place among the all-county runners.
Kadien Kimble was the highest finished for North Putnam, finishing 14th on the night. Cloverdale was led by Andrew Monnett in 21st and Joe Rutenbert in 23rd place.
At South Putnam
Putnam County Boys' Cross Country Meet
1. South Putnam 29, 2. Greencastle 32, 3. North Putnam 87, 4. Cloverdale 95
1. Barr (SP) 17:21; 2. Hudson (G) 17:24; 3. Freeman (SP) 17:45; 4. Secrets (G) 18:17; 5. Spear (NP) 18:36; 6. Lewis (G) 18:50; 7. Franklin (SP) 18:59; 8. Lund (SP) 19:03; 9. White (G) 19:11; 10. Allen (SP) 19:16
1. Greencastle 17, 2. South Putnam 45, 3. Cloverdale 85, 4. North Putnam INC
1. Gellman (G) 12:23; 2. Wilson (G) 12:29; 3. Crawley (G) 1:39; 4. Clearwaters (SP) 13:10; 5. Featherson (G) 13:12; 6. Kendall (G) 13:22.34; 7. Jones (G) 13:22.94; 8. Baugh (SP) 13:26; 9. McCarty (G) 13:30; 10. Fanning (SP) 13:35
Next Meet: The WCC Cross Country meet takes place Saturday at South Putnam High School starting at 10 a.m.