Caitlin Rhodes (16) and Luci Grigg (16) won the rebranded contest at the Amuri A&P Show at the Rotherham Showgrounds on Saturday.
''I'm stunned,'' Luci said.
''I was a last-minute entry after Caitlin's original teammate broke his arm a week out from the event.
''Caitlin asked if I'd be keen to take his place and I said yes.''
About 60 high school pupils from across the Tasman region worked in pairs to tackle a raft of challenges.
The modules tested the pupils' practical and theoretical skills, and included a quiz hosted by Te Radar.
''I really enjoyed the challenges, especially the module about the digestive tracts of ruminant and monogastric animals,'' Luci said.
Caitlin and Luci were the second all-girl team to win a Junior Young Farmer of the Year regional final this year.
''These students are operating at a very high level,'' Te Radar said.
''The questions they were answering in the quiz were taken from previous FMG Young Farmer of the Year regional finals.''
Charlie Kinney (17) and Jack Stokes (17), from St Andrew's College in Christchurch, came second.
Charlie comes from Culverden, while Jack is from Waikuku in North Canterbury.
Both teams have qualified for the Junior Young Farmer of the Year grand final in Hawke's Bay in July.
The Junior Young Farmer of the Year competition was formerly known as TeenAg.
Seddon School claimed first and third in the AgriKidsNZ contest, and Oxford Area School placed second.
In that regional final almost 80 pupils, working in teams of three, took on a series of eight fun modules.
The top seven teams went head to head in a race-off.
''The aim of the event is to get kids excited about opportunities in the primary industries,'' competition co-ordinator Jake Lonergan said.
-By David Hill
