A second-place finish for the all-Kiwi combination of Shane van Gisbergen and Earl Bamber means van Gisbergen has opened up a 55-point championship lead.
Scott McLaughlin, meanwhile, had to settle for a distant fourth, following a quiet weekend for his Shell V-Power Racing at Tailem Bend in late August.
“It was a very strange weekend at Sandown and I don’t really understand what has gone on,” Murphy explained.
“Red Bull Holden Racing, regardless of what they might say about the fact they don’t have an advantage, certainly look like they have managed to do what they normally do, which is to push the envelope to the absolute limit.
“They put an enormous amount of time and resource into it, which is more than just about everyone except maybe the Penskes of the world, and they have got their cars working so very, very well.
“With the ZB Commodore, to me it looks like they have used the rule book and their resources to come up with something better than everyone else.
“The Red Bull Holden guys have done a great job to find a few things with their car that have conspired to do what they did on the weekend but it was aided by the fact that the DJR Penske guys were also-runs.”
McLaughlin and Alex Premat were the best of the Fords, 25 seconds behind Whincup at the end of the 161 laps.
In Saturday's regular ARMOR ALL Qualifying session, McLaughlin only managed the 14th fastest time.
The sister entry of Fabian Coulthard and Tony D'Alberto finished the race seventh.
“Nothing they did on the weekend makes any sense to me in respect to their speed,” Murphy said of the Falcon squad.
“If you go back to Sydney Motorsport Park in August, Scott McLaughlin was on pole position again and was leading that race and really only lost it because of the Safety Car at the end.
“He had really good speed compared to the Red Bull Holden Racing Team.
“Then they went to Tailem Bend and they really struggled there. You can put that down to a bit of quirk [and lack of speed on the hard tyre] in their season and they didn’t quite get it right.
"But Sandown, there was no excuse about why they shouldn’t be back on form.