The 31-year-old lines up for his 10th season with Triple Eight this year in a partnership that has yielded six of the last seven championships.
The contract announcement has coincided with the team showing off a mildly revised livery ahead of the weekend's pre-season test at Sydney Motorsport Park.
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Having agreed only a one-year extension this time last year, Whincup says the length of the new deal reflects his outlook on the championship's prospects.
“I'm obviously very excited to renew my contract with Triple Eight,” Whincup said.
“The decision firstly came from the strength of the V8 Supercars category; I think there are some exciting times ahead, especially coming into the phase with the new television deal and later the new generation cars.
“I can see a really strong future for the series.
“Secondly, I'm honoured that Triple Eight, the best team, wants to retain my services, which I try very hard to maintain, to showcase their engineering.
“A one year contract seemed like a bit of a waste of time with the changes coming in 2017, so the decision was to renew for three years so that I'll have at least two years with Triple Eight in the new generation cars.”
“We're extremely happy that Jamie is staying with Triple Eight for the foreseeable future,” he said.
“Though he has nothing to prove with us, he continues to push the boundaries with the utmost professionalism, which is exactly the mentality and approach of Triple Eight.
“Meanwhile, I'm looking forward to sitting down with Craig very soon to discuss 2016 and beyond with him.”
Lowndes will this weekend have his first chance to work alongside new race engineer Grant McPherson, who replaces the Porsche World Endurance Championship-bound Jeromy Moore.
“We've got a great season ahead and I'm really looking forward to getting stuck into it with my new engineer in Grant McPherson,” said Lowndes.
“It's a fresh start and also a very exciting start. We're going to have to work very closely and quickly together so he's got confidence in me, I've got confidence in him and then we can hit the ground running.”