The News International plant, based in Docklands, pipped The Northcliffe Press Staverton, which was highly commended for The Citizen, to the title at the ceremony on Wednesday night.
NI's Knowsley plant took third place, also for production of The Times.
Judges including Colin Brooks, Trinity Mirror Printing (Watford) director and general manager, David Wells, Leeds Web managing director, and Gillian de Bono, editor of Financial Times supplement How to Spend It, praised Wapping for its "good consistency in printing detail, especially in the images".
The evening's National Newspaper of the Year award went to The Daily Telegraph, with The Independent and The Times in second and third place respectively.
The Citizen also walked away with the Regional Newspaper of the Year award, for its layout, production and "crisp fold quality".
Ray Tindle, proprietor of Tindle Newspapers, won the Personality of the Year award for his lifetime achievement in the newspaper industry.
* The Times completed the week with another good showing in the monthly ABC figures, released today, with a 2.2% monthly increase in circulation to 685,448.
The Independent added 1.35% to its figure to reach 262,004, while the total circulation for the quality papers increased by 0.5% in the month, and 3.2% year on year, to reach 2.8m.
The success of the quality titles was not reflected in the tabloid sector, which has recorded a 5.1% drop in circulation year-on-year to 6.3m.
In the mid-market sector, both the Daily Express and The Daily Mail lost readers, to post a 1.8% year-on-year drop in daily sales to 3.3m.
Story by Josh Brooks
