Norsqui, winner of the Adelaide Cup (3200m) which was downgraded to Group Two in recent years, held second, three-quarters of a length from the winner with Aliyana Tilde a half head third.
As usual, Williams stayed at home, but his son and partner Nick was on hand for the family's third Sydney Cup after Gallic (2007) and Major Drive (1987).
"It's fantastic," Williams said.
"Hugh was very confident before the race and summed up the race.
"He's the best jockey in Australia and showed why.
"It's great to be here and be part of the carnival at Randwick with the new grandstand and all that goes with it."
Bowman also rode Mourayan last week when the horse ran fourth to Kelinni in the Chairman's Quality.
The win was Bowman's fifth Group One for the autumn carnival and second on the final day.
He won the Chipping Norton Stakes on Shoot Out, the Vinery Stud on Norzita, the BMW on Fiveandahalfstar and Reliable Man in the Queen Elizabeth Stakes.
Norsqui's trainer Walter McShane was proud of his horse.
"It was his first time right handed and he was great," McShane said of the Tasmanian gelding.
"I don't know where we go from here. He's probably going to get a lot more weight in these races now. We'll go home and think about it."
Maluckyday, runner-up in the 2010 Melbourne Cup, and his stablemate Niwot, last year's Sydney Cup winner, finished seventh and ninth respectively.
The Chris Waller-trained winner Reliable Man upset triple crown-winning Kiwi colt It's A Dundeel in the $500,000 Queen Elizabeth Stakes at Randwick yesterday.
But in a worrying postscript to the group one, the French Derby winner had to be led back to the saddling enclosure without jockey Hugh Bowman.
The entire was put into a horse ambulance in what chief steward Ray Murrihy said was a precautionary measure.
Asked if he knew what happened to his mount, Bowman said: "I've got no idea, but he is clearly lame."
Reliable Man was having his second Australian start under the care of Waller, who 24 hours earlier avoided a penalty over a spate of positive swabs in his stable.
An inquiry found that a contaminated batch of feed led to three Waller-trained horses testing positive.
"The last 24 hours have obviously been tough, but I haven't looked forward to a day's racing as much as today," Waller said.
Given a perfect run by Bowman, Reliable Man shot to the front at the 200m and he had 2 lengths in hand at the finish over It's A Dundeel.
As is customary, It's a Dundeel settled last and he made his run four wide on the bend, but was unable to bridge the gap on the winner.
South Australian galloper Happy Trials finished third.
-AAP
