Bevin, 27, riding for the CCC Team, capitalised on confusion in the peloton sparked by a mass crash inside the final kilometre of the 122km second stage to power home in the finish.
The Kiwi unleashed a sprint on the uphill 700m finishing straight to reel in Spain's Luis Leon Sanchez before holding off Australian star sprinter Caleb Ewan and Slovakia's former triple world champion Peter Sagan at the line.
The stage win gave Bevin a 10-second time bonus, lifting him into the overall lead of the race, five seconds ahead of Italy's Elia Viviani, who won Tuesday's stage one but could only manage seventh the next day.
Bevin holds a five-second lead over Viviani in the race general classification with Ewan in third place ahead of Germany's Max Walscheid (Team Sunweb).
Walscheid finished 23rd in Wednesday's stage through South Australia's famous Barossa Valley wine country in scorching temperatures of 40 degrees Celsius (104 Fahrenheit).
"I got to pick a pretty good line in the hard, draggy finish. Once Sanchez was off the front in the final it gave me the perfect springboard and I just went long," Bevin said.
"It was definitely a gamble, you could take five seconds today and lose two minutes in three days' time but that's bike racing, we're here to try to win it."
Bevin, whose previous race best in the UCI season-opening tour was 10th in 2016 and 11th last year, avoided a pile-up in the peloton which blocked the road to the Angaston finish line.
The crash left around 25 riders to contest the finale with Bevin surging from deep before dipping in behind Sanchez's slipstream and crossing the line with enough time to clench and raise his hands in celebration.
His victory is CCC Team's maiden World Tour victory and his first triumph outside of a national championship since winning stage four of Australia's Herald Sun Tour in February 2015.
The peloton once again had to endure brutal temperatures on the stage, which was cut pre-race by 26.9km because of the extreme weather conditions.
Australia's Jason Lea (UniSA-Australia) retained the King of the Mountain jersey after stage two from Kazakhstan's Artyom Zakharov (Astana) and Bevin.
Viviani edged Bevin for the sprint leader's jersey by a point and another to Germany's Phil Bauhaus (Bahrain Merida Pro Cycling Team).
Thursday's Stage 3 launches from Lobethal into a challenging six-kilometre hills circuit that finishes in Uraidla.
Results after the 122.1km second stage of the UCI Tour Down Under from Norwood to Angaston in South Australia on Wednesday:
1. Patrick Bevin (NZL/CCC Team) 3 hr 14 min 31 sec
2. Caleb Ewan (AUS/Lotto Soudal) same time
3. Peter Sagan (SVK/BORA-hansgrohe) s.t.
4. Danny Van Poppel (NED/Team Jumbo Visma) s.t.
5. Jasper Philipsen (BEL/UAE Team Emirates) s.t.
6. Phil Bauhaus (GER/Bahrain Merida Pro Cycling Team) s.t.
7. Elia Viviani (ITA/Deceuninck-Quick-Step) s.t.
8. Luis Leon Sanchez (ESP/Astana Pro Team) s.t.
9. Kiel Reijnen (USA/Trek-Segafredo) s.t.
10. Kristoffer Halvorsen (NOR/Team Sky) s.t.
1. Patrick Bevin (NZL/CCC Team) 6 hr 34 min 03 sec
2. Elia Viviani (ITA/Deceuninck-Quick-Step) at 5 sec
3. Caleb Ewan (AUS/Lotto Soudal) +9
4. Max Walscheid (GER/Team Sunweb) same time
5. Artyom Zakharov (KAZ/Astana Pro Team) s.t.
6. Jason Lea (AUS/UniSA-Australia) +10
7. Michael Storer (AUS/Team Sunweb) s.t.
8. Peter Sagan (SVK/BORA-hansgrohe) +11
9. Jakub Mareczko (ITA/CCC Team) s.t.
10. Jaime Castrillo (ESP/Movistar Team) +12
1. Elia Viviani (ITA/Deceuninck-Quick-Step) 24 pts
2. Patrick Bevin (NZL/CCC Team) 23 pts
3. Phil Bauhaus (GER/Bahrain Merida Pro Cycling Team) 22 pts
King of the Mountain
1. Jason Lea (AUS/UniSA-Australia) 20 pts
2. Artyom Zakharov (KAZ/Astana Pro Team) 12 pts
3. Patrick Bevin (NZL/CCC Team) 4 pts