The result confirmed the recent dominance of Tunisia over Egypt having beaten them home and away in 2015 qualifying. It was Youssef Msakni who provided a sublime through ball for Khennisi to find the back of the net.
The Tunisians bossed the game and didn't allow the AFCON runners-up to pose any theat whatsoever.
Egypt coach Hector Cuper admitted that his side didn't put up a strong challenge against the Tunisians.
"We didn’t play well today and the performance was average in the first half. It was hard to get back in the game. The conditions were hard and the professionals didn’t play well. We'll try to get back in the future and won’t lose our focus. The Tunisian team are strong and deserved the win but qualifying isn’t done yet," said the experienced Argentine.
Tunisia top Group J with three points and Niger and Swaziland have one each after a 0-0 draw in Niamey at the weekend.