Rebel Labour MPs were unhappy decisions over projects such as power stations and airports would move from elected to unelected decision makers, and had table an amendment to the Planning Bill that would have seen the ultimate decision on schemes resting with Parliament.
However, the amendment was defeated this afternoon, with 303 MPs voting against it and only 260 in favour.
The IPC will have 20 to 30 members that will be appointed by Department of Communities and Local Government (DCLG).
From these members, panels of three commissioners will be appointed to oversee the biggest infrastructure schemes. Individual commissioners will consider smaller schemes.
Officials at the assured NCE that civil engineers would be part of the IPC.
The new legislation will open the door to much faster planning for major infrastructure projects, such as power stations or transport projects.
However, the Government only won by incorporating into the Bill two amendments to make the IPC proposal more palatable to rebel Labour MPs.
First, the IPC will be legally required to take into account a report of local community views produced by the local councils concerned.
Second, if a developer applies for a compulsory purchase order, then any affected parties have a right to force the IPC to hold a public hearing at which they must be heard.
The Bill will now move to the House of Lords for scrutiny.