Wiggins, a four-time Olympic champion and former Tour de France winner, had hoped to win his first Commonwealth Games title after three silver medals.
But the England team of Wiggins, Steven Burke, Ed Clancy and Andy Tennant finished more than five seconds adrift.
Wiggins said: "We were all on different levels."
Wiggins ready to 'graft' for RioThe 34-year-old will not compete in any more events at this year's Games, but said he was looking ahead to the Rio 2016 Olympic Games.
"Four weeks ago we sat in a room for the first time in six years and wondered how far we can go," Wiggins said.
"We've had limited preparations for this and hopefully we will look back in two years' time with gold medals around our necks thinking 'this was the starting point in Glasgow'.
"I've said all along that the track was always what I was going to go back to. I need to put some muscle on and get stronger.
"It's going to be two years of graft and we can't underestimate how much work we have ahead to get in the right place for Rio."
Clancy and Burke were part of the team that won gold for Great Britain at the 2012 Olympics in London, setting a new world record in the process.
However, Clancy was also in the British team that finished a disappointing eighth at this year's World Championships in Colombia, an event in which Australia triumphed.
Kuala Lumpur 1998 - silver in team pursuit
Manchester 2002 - silver in team pursuit
Manchester 2002 - silver in individual pursuit
Glasgow 2014 - silver in team pursuit
And England were no match for the Australian foursome of Jack Bobridge, Luke Davison, Alex Edmondson and Glenn O'Shea at the Sir Chris Hoy Velodrome.
Australia, who finished second at the 2012 Olympics, clocked three minutes 54.851 seconds - a new Commonwealth Games record - against England's 4.00.136.
New Zealand, who were narrowly beaten by England in qualifying, beat Canada in the bronze medal race, catching them at the halfway point.
Wiggins last competed in a Commonwealth Games in Manchester in 2002.
The 2012 Tour de France champion was controversially overlooked for this year's race, which is taking place at the moment, with Team Sky choosing to build their side around fellow Briton and last year's winner Chris Froome, who crashed out in the first week.
Londoner Wiggins plans to concentrate on the track for the next two years, before making a final bow at the 2016 Olympics in Rio.
Australia, who finished second at the 2012 Olympics, clocked three minutes 54.851 seconds, a new Commonwealth Games record 
England were no match for the Australian foursome of Jack Bobridge, Luke Davison, Alex Edmondson and Glenn O'Shea 
The England team of Wiggins, Steven Burke, Ed Clancy and Andy Tennant finished more than five seconds adrift. 
"I've said all along that the track was always what I was going to go back to. I need to put some muscle on and get stronger," Wiggins said afterwards.
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