The top three in the general classification, Bouchard (BH SR Suntour KMC) Anton Sintsov (JBG-2), and Andrew L'Esperance (Forward Racing-Norco) all crossed the finish line together at Lake Tinaroo in 4hr 9min 37sec leaving the general classification and time gaps unchanged.
Multiple Tour de France stage winner Erik Dekker, racing in the A3 category, finished in fourth position ahead of Australian A2 racers Ondrej Slezak (Quantum) and Alex Malone (Cyclist Magazine).
In the overall women's field, Haley Smith (Norco Factory Team) finished in 4hr 32min 6sec ahead of Swiss amateur rider Daniela Erni Ruoss (2XU)) and Australian Kylie Lindsay.
After a neutral start in Cairns, riders arriving at the finish at Lake Tinaroo on the Atherton Tablelands would be satisfied with finishing a tough 79km stage with repeated big climbs adding up to 2100 metres of total elevation.
The "Croc" is nothing but an adventure and Stage 2 turned up a surprise after a locked access gate prevented the lead car from continuing, forcing riders to rely on GPS coordinates to navigate their way for several kilometres.
The unexpected event saw 13 riders miss a crucial turn adding 5 to 8km to their race distance before rejoining the correct track.
"This was a very unfortunate situation, especially as we relied on our permit documentation, however, we understand it was a mere miscommunication that caused the Sunwater gates to be locked today," race organiser Gerhard Schönbacher said.
"I have been informed that the 13 riders were able to provide GPS information of their race times and based on their additional kilometres had an average time deducted from their race time today."
Stage 3 will take the riders on a 100km route with 2600 metres of elevation through the Baldy Mountain Forest Reserve to Tepon Equestrian Park.