Using the same strategy as before, the BCX duo were again able to build up a lead during the first half of the 48km final stage in the Wellington area en route to winning in 1:49:34.
On the day, they were followed by Versus Socks' Jurgens Uys and Nicol Carstens (1:51:07) and TIB Insurance-Momsen Valley Light's Andrew Hill and Marco Joubert (1:52:34).
Woolcock and Kruger sealed the title with an overall racing time of 6:18:53, ahead of Hill and Joubert (6:28:01) and Uys and Carstens (6:30:57).
Sweden's Jennie Stenerhag added the women's title to the Cape Epic crown she won last month when she and her Cape Brewing Company teammate Katie Lennard completed a comfortable overall victory in 7:38:48.
Reflecting on the race, Woolcock said he felt their success had been built on the opening stage when they created a three-minute lead which they gradually increased.
"We came here with a goal of winning the race and we always knew it would be important to get a gap on the opening day," he said.
"Besides giving you a buffer, it also gives you a mental head start on the rest if you can show you are the strongest.
"We went hard from the start on the first day on probably the toughest stage of the three, so that set up our advantage."
Kruger said they began the final leg with the aim of staying near the front and avoiding mechanicals or crashes.
"We managed to get a gap fairly early on and then rode at a steady tempo and it was cool to win our third stage in a row," he said.
"As we both come from the region - I'm from Paarl and Waylon from Stellenbosch - it was very satisfying to win this title. It gives us a positive attitude looking ahead to our next races."
Kruger said they had particularly enjoyed the overall atmosphere of the Liberty Winelands Encounter, in partnership with STANLIB.
"Generally it was quite a relaxed vibe, some really good routes, and we could not have asked for better weather. It's a great event and hats off to the organisers for their hard work."
Stenerhag was pleased with her effort after she and Lennard won the final stage ahead of Companero's Jana Kruger and Ilse Viljoen.
"I particularly enjoyed riding with Katie, who was always very good on the technical sections. Overall it was a good experience and the organisation was great."
She said she would be riding in the TrailSeeker Series in Tulbagh next weekend before returning to Europe.
In the mixed category, dormakaba RA's Corne Barnard and Vera Adrian won their third stage in a row in 2:03:10 to head the general classification on 7:07:28.
Home Ice Cream's Matthew Stamatis and Carmen Buchacher were second on the stage in 2:06:34 and overall in 7:16:12, followed by Bestmed-Ellsworth-ASG's Pieter Seyffert and An-Li Kachelhoffer in 2:13:58 and 7:38:48.
Caption: HB Kruger (front) and Waylon Woolcock, of BCX, lead the way en route to their third stage win and overall victory in the Liberty Winelands Encounter, in partnership with STANLIB, near Wellington in the Boland today. Photo: Ewald Sadie