The team, lead by group production director Chris King, picked up its prize at the annual PPA Magazine Production Awards held at the Millennium Mayfair Hotel in London.
Haymarket, the UK's largest independent publisher and parent of PrintWeek, fought off competition from Emap, NatMags, Reed Business Information and William Reed to win the award.
"It's great news to win this award, which recognises the hard efforts, many changes and many improvements introduced by production over the last few years," said King.
PrintWeek's former editor at large, Jo Francis, was named Industry Personality of the Year in recognition of the contribution she made to print journalism during her 11 years with the magazine. Francis left PrintWeek in July to join graphic arts PR agency AD Communications.
Other significant wins included Stones the Printers, part of Goodhead Group, which landed the Magazine Printing Company of the Year prize.
Stones managing director Simon Hunt said he was "chuffed" at the win. "It's a hugely competitive marketplace. All we hear is price, price, price but we don't lose sight of the fact that price is only part of it."
The awards ceremony was held after the Magazine Production Conference.
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