He used his access to security databases to include his wife on a watch list of people banned from boarding flights into Britain because their presence in the country is 'not conducive to the public good'.
As a result the woman was unable for three years to return from Pakistan after travelling to the county to visit family.
The tampering went undetected until the immigration officer was selected for promotion and his wife name was found on the suspects' list during a vetting inquiry.
The Home Office confirmed today that the officer has been sacked for gross misconduct.
The incident is likely to raise new questions over levels of efficiency in the UK Border Agency, the organisation formed nearly three years ago by then Home Secretary Jacqui Smith to take over all immigration controls.
It has been criticised for poor performance by the Parliamentary Ombudsman and has suffered its share of humiliating incidents - for example the incident 19 months ago when an illegal immigrant escaped from the channel tunnel port at Folkestone by clinging to the underside of a bus carrying Border Agency staff.
The Agency is charged with putting into operation the Coalition's policy of reducing numbers of workers from outside Europe allowed into Britain.
A spokesman said: 'We expect the highest levels of integrity. Allegations of misconduct are thoroughly investigated and we always take action swiftly where we find members of staff who have abused their position.
'On the extremely rare occasions where this occurs, the strongest action is taken.'
The officer in the latest incident to come to light was employed by a unit maintaining watch lists.
He is understood to have worked at the Agency's headquarters at Lunar House in Croydon, South London.
His wife visited family in Pakistan but when she tried to return to Britain she was not allowed onto the aircraft. Airline and immigration officials refused to explain to her why.
She was forced to remain in Pakistan for three years until her husband's manipulation of the suspect list came to light.
He is understood to have applied for a promotion that would have meant a higher level of security clearance.
During the vetting process the name of his wife was discovered on the suspect list, to the surprise of security staff.
When questioned, the officer confessed to his alteration of the lists and was sacked.