MPs voted Tuesday night for a total ban on smoking in all bars, clubs and restaurants.
The other options, to exempt private clubs and also licensed premises serving food, were dismissed by a margin of 200 votes.
Mark Hastings, spokesperson for the British Beer and Pub Association, welcomed a total ban as opposed to an exemption for private clubs. He said such clubs served around 1.2bn pints of beer every year and it was essential to have a "level playing field" with others in the industry.
Hastings, however, said the ban could make things tough for many in the pub trade.
"Now the real hard work begins, preparing our customers and pubs for this cultural shift. There is still the prospect that hundreds of community pubs will close and people will lose their jobs."
Some firms, such as brewer and pub owner Greene King, have already begun converting premises to provide outside areas for smokers.
The government had initially been against a total smoking ban, but has been beaten down in recent weeks by a Commons Health Select Committee and even the health secretary, Patricia Hewitt, herself.
They argued it was the best way to improve public health. A ban is already set to come into force in Scotland this year.
The likely effects of a smoking ban on pub and drinks sales have been widely debated in the industry over the last year.
The JD Wetherspoons pub chain, which has already introduced some entirely non-smoking pubs, said recently that a seven per cent like-for-like sales decline at its non-smoking pubs in the first quarter had continued. Like-for-like sales were down 0.3 per cent across its pubs for the 24 weeks up to 8 January.
Wetherspoons is reviewing its plans to open more non-smoking pubs and will make an announcement in its first half interim results, due 3 March.
One potential problem for pub owners is that a pub smoking ban may quicken an already growing trend for drinking at home.
The amount of alcohol consumed at home rose nine per cent between 2004 and 2005, according to the BBPA. It also cited government statistics published last August, revealing supermarkets now account for 40 per cent of UK beer sales, 76 per cent of spirits sales and 84 per cent of wine sales.