However it was Taupo teenager Greg de Latour who muscled his 300cc Beta machine into the battle of champions, making up time from a delay at the start to pass Whitaker near the end of the final.
The tight course and 12-rider fields meant a good start was crucial as the racers tackled multiple man-made hazards such the "Death Trap", "Bike Breaker", "Rocky Mountain" and "Devil's Hairpin" - all made slippery by light drizzle.
Birch was happy with his decision to ride a four-stroke KTM 350 EXC-F.
"The two-stroke would probably be better once you are going, but the four-stroke really jumps off the start," he said.
"I really enjoyed the event. I'm more used to six or eight-hour events while this is intense short bursts and quite stressful."
Birch will begin the defence of his national enduro title when Whangamata hosts the opening round on February 22.
Later in the year his programme will take him to extreme events in South Africa, Turkey, Romania, Ecuador and Australia.
De Latour has been a regular finalist at the endurocross and his second placing was his best effort yet, passing Whitaker late in the race.
"I had trouble with the starts all day," said De Latour. "It was the same in the final and I was last away but then I rode smoothly and didn't make any mistakes."
Smith was another to make a bad start and get delayed at an early traffic jam before riding through the pack on his Yamaha YZ250 to gain third when he passed Whitaker on the final lap.
Whitaker (Husaberg FE 250) and Birch had been the race winners at the semifinal stage of eliminations and Whitaker ran second for the early part of the race but eventually finished fourth.
"I was quite close behind Chris in second and then I got hung up behind a lapped rider and lost ground. After that I tried to make up time but I made too many mistakes," said Whitaker.
The only local rider to reach the final was Te Puke's Phil Singleton (Honda CRF250) who rode to a sixth place finish behind Pukekawa's Anthony Parker (KTM 250).
The hard luck riders were Auckland teenager Liam Draper who had bike troubles and didn't make the start of the elimination rounds and top contender Chris Power (Auckland).
Power (Yamaha YZ250) had the speed to be a podium contender but on lap two of the final his bike tangled in a tarpaulin that was part of the "Death Trap" hazard, which combined tyres and a water splash.
Te Puke A&P Show Endurocross:
Final (10 laps): 1 Chris Birch (Glen Eden) KTM 350 EXC-F, 8min 30secs; 2 Greg de Latour (Taupo) Beta 300, 8m 50s; 3 Adrian Smith (Awakino) Yamaha YZ250 8m 56s; 4 Jake Whitaker (Wellington) Husaberg FE 250, 8m 59s; 5 Anthony Parker (Pukekawa) KTM 250 EXC, 9 laps; 6 Phil Singleton (Te Puke) Honda CRF250, 9 laps.