The scheduled match was called off because of security situation and tension in Lahore after violent protests by Christians continued for the second day today.
A senior PFF official said that the match was called off after consultations with FIFA.
"The match has been called off after consultations with the FIFA match officials," PFF Marketing Director Sardar Naveed Haider said.
Haider said a pre-Olympic qualifying round group tournament in Lahore from March 23 had also been called off due to the security situation.
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Earlier, uncertainty hovered over the fate of the match due to yesterday's suicide bombings at two churches.
The PFF said the situation was unfortunate and it was true that the Yemen contingent had been anxious and tense about playing the match.
FIFA match commissioner John Windsor of Malaysia had cancelled the pre-match news conference of both the teams.
Reports from within the Yemen team were not very positive as they said their players were not keen on playing the match.
Pakistan needed a 2-0 win to qualify for the next round, after they were beaten in the first leg 3-1.
Since the bombings on the two Churches yesterday violence has broken out in the city with angry Christians taking to the roads to protest failure of the government to provide them security.