To their credit, Burgess, Rotorua's Nathan Sharland and Auckland's Callan May never gave up.
After the race, Clarke opted to allocate them each a time; the average time of their other four laps.
Burgess went on to win the overall with Taupo's Greg De Lautour (KTM 350EXCF) taking second and Taranaki mud specialist Tony Parker (KTM 350XCF) third overall.
The win, coupled with his third placing at the series opener, puts Burgess 10 points out in front of De Lautour, with May holding on to third spot overall for the series.
The intermediate grade riders were up against it from the start as the experts did their best to destroy the track in front of them. Putaruru's Kian Scherer celebrated the win, with Hamilton's Craig Cameron second and Waihi KTM rider Steve Price taking third spot.
"The course was a real challenge, so anyone who finished a couple of laps should be proud of themselves," said Clarke.
The earlier junior race was run on a near-perfect track with the skies only opening up near the end of the 90-minute race.
Auckland's Jake Wightman wrapped up his second win of the series on his KTM 125EXC, with Oparau's James Scott not far behind.
In the minis race, Oparau's Hunter Scott cleaned up again, winning the race by more than a lap from Patumaohe's Joshua Hilton, with Taupo's Will Yeoman rounding out the top three.
The third and final round of the series is set for Ohakuri, also just south of Tokoroa, on June 15.