The crucial match was abandoned late in the second half, with the government official among those who were caught up by the unrest in the stands
The second leg of the tie between Senegal and Ivory Coast had to be abandoned minutes from the end after crowd trouble erupted, which saw missiles thrown on the pitch and small fires started in the stands at Stade Leopold Senghor.
The Elephants were ahead 2-0 on the night, thanks to Didier Drogba's double, with the Teranga Lions trailing 6-2 on aggregate, before the match was called to a premature halt.
"He [Gakou] has been hurt by a stone and was evacuated," a doctor was quoted as saying by AFP.
"We had three cases of wounds that required stitches, and four or five cases of discomfort or pain. But there were no serious injuries, people were not trampled."
Senegal's official news agency APS later remarked: "The match was halted and the Lions of Senegal will not qualify for the 2013 Africa Cup of Nations."
No comment has been made by the Confederation of African Football (CAF), though the result is expected to stand, with Ivory Coast, runners up in 2012, likely to be named in the main draw that will be held later this month.