Green laser pointers were directed at several Egypt players and the goalkeeper during the shootout, along with the game, after Senegal had won 1-0 after 120 minutes to draw the tie 1-1 on aggregate.
Salah was one of four players to miss the opening four spotkicks of the shootout before Liverpool teammate Sadio Mane converted the decisive penalty for a 3-1 win.
The win clinches Senegal’s third World Cup berth and back-to-back qualifications for the first time. The triumph comes only six weeks after Aliou Cisse’s side beat Egypt to win the African Cup of Nations for the first time.
Egypt coach Carlos Queiroz said: “There is not much to say just nice words for the players for the game they played. Congratulations to Senegal.”
Elsewhere there were ugly scenes in Abuja post game after Ghana knocked out Nigeria on away goals following a 1-1 draw.
Arsenal’s Thomas Partey had put the Black Stars ahead in the 10th minute with William Troost-Ekong’s penalty not enough for the hosts.
After the game, angry Nigeria fans throw water bottles at the triumphant Ghana players, coaches and staff as they left the pitch.
Meanwhile the other nations to clinch qualification in Africa were Morocco (5-2 on aggregate over DR Congo), Cameroon (on away goals against Algeria) and Tunisia (1-0 on aggregate against Mali).