The amendments will also see water companies become statutory consultees for any shale gas planning applications.
In a heated debate, Labour MPs cheered when their 13 proposals were adopted by the government and added to the Bill.
The measures state that fracking cannot take place unless: an environmental impact assessment has been carried out; independent well inspections are carried out; a 12 month monitoring period at any potential fracking site is completed; and measurement and monitoring of fugitive methane emissions are published.
The new clause 19 to the Bill also states that fracking is banned in groundwater protection zones, within or under protected areas; at depths of less than 1,000 metres; unless planning authorities consider the cumulative effect of fracking activities; and unless community benefit schemes are provided by the fracking companies.
Under the amended Bill, fracking will also be prevented unless: residents in the affected area are notified on an individual basis; the substances used are subject to approval by the Environment Agency; land is left in a condition required by the planning authority; and unless water companies are consulted by the planning authority.
Shadow energy secretary Caroline Flint said: “This is a huge U-turn by the government and a big victory for the protection of Britain’s environment.”
Energy minister Amber Rudd also told MPs there would be an “outright ban” on fracking in National Parks.
A cross-party proposal for a 30 month moratorium on fracking while an assessment into its environmental impact is carried out was voted down by 308 votes to 52.
Chief executive of the UK Onshore Oil and Gas association Ken Cronin said: “It is good news that MPs have rejected the misguided attempts to introduce a moratorium on hydraulic fracturing.
“Most of the amendments agreed are in line with best practice in the industry or codify the directions of regulators, which the industry would naturally comply with.
“We now need to get on with exploratory drilling to find out the extent of the UK’s oil and gas reserves.”