Whincup leaves the Coates Hire Ipswich 400 with a 15 point lead over Winterbottom, who lost his position at the top of the order thanks to a tyre failure in Race 25.
The move follows a strong run of form for Whincup, who has won six of the last nine races following a mixed start to the season.
Courtney meanwhile jumped from sixth to fourth in points with his second win of the season and is now just 192 points adrift of the lead.
While the HRT looks increasingly threatening as it continues an aggressive development schedule under Adrian Burgess, Whincup is downplaying the factory Holden team's title credentials.
“As far as race wins go, absolutely those guys will come on strong and be very hard to beat,” said Whincup of the HRT.
“But I still think that FPR do a good job and they'll be strong come the end of the year. They've been around a long time.
“I just respect the FPR guys,” he continued.
“They were 200 points up the road for a reason. They did a bloody good job.
“That's why I still think they're the team to beat.
“They didn't get there for no reason and I think a bit of respect is due in that regard.”
While Courtney is full of enthusiasm for his team's progress, the 2010 champion isn't getting carried away with talk of a second title.
Last year saw Courtney enter the three-event Pirtek Enduro Cup just 160 points behind Whincup and leave 640 adrift after a string of disasters.
“As a team we're just getting stronger and stronger,” said Courtney of the HRT's progress.
“We had a one-two at the last round (Townsville) and before that in Darwin we were quite strong.
“It's becoming easier for us to be qualifying at the front and racing at the front, whereas in years gone by we were flogging around mid-field and weren't achieving anything.
“This year we really have the roots in and the thing is starting to grow and produce some fruit.
“I think this is the most successful year that HRT has had since I've been here, definitely. It's been a long time and a long building process.
“There is a long way to go in the championship, we've still got three rounds (Pirtek Enduro Cup) with 300 points (each) where some other boneheads (co-drivers) will jump into the car with us.
“Anything can happen, we all saw that last year, so at this time of year we're all pretty happy but I think coming out of the Gold Coast it might be a different story.”
Winterbottom meanwhile will be looking to recapture the ascendancy from Whincup at the next event on the calendar at Sydney Motorsport Park; the last prior to the endurance races.
“We'll keep fighting of course and we're not doing too much wrong at the moment,” he said after Race 25.
“It was a points hit but if we are quick enough we'll make it back up there easily enough.
“Chaz was quick and there are positives to take away so we'll bounce back.”
The Sydney meeting will take place on August 21-22 and see both the hard and soft tyres in action.