Moussa Sow's second-half penalty was not enough to overturn the first-leg deficit as Sabri Lamouchi's side sealed qualification for Brazil 2014 with a late strike
Sabri Lamouchi's side headed into Saturday's game having eased to a comfortable 3-1 win in the first leg last month, although Senegal still had half a chance by virtue of their away goal.
The Elephants completed the job with a solid performance, although they were pushed hard before finally confirming a 4-2 aggregate victory.
The second leg was played at the Stade Mohamed V in Casablanca as Senegal lost home advantage as punishment for crowd trouble in an Africa Cup of Nations play-off tie between the two sides back in October 2012.
However, that did not appear to affect them, and they dictated play for the majority of the game as they looked to qualify for the World Cup finals for the first time since 2002.
For all their pressure, it took Senegal until the 77th minute to make the breakthrough, with Sow's penalty giving Alain Giresse's side brief hope.
But the crucial second goal did not arrive, and their hopes were finally killed off when Kalou struck in injury time to send Cote d'Ivoire to next year's finals in Brazil.
Senegal coach Giresse made five changes to the side that lost the first leg, with midfielders Salif Sane and Sadio Mane among those to come into the side as the likes of Sow and Mohamed Diame dropped to the bench.
Cheick Tiote and Geoffrey Serey Die both missed out due to suspension for Ivory Coast, who maintained a front three of Gervinho, Kalou and Didier Drgoba.
Giresse's men made the better start, but it took them until the 14th minute to create the game's first real chance as Newcastle United striker Papiss Cisse saw his goalbound header hooked away by Drogba.
Cote d'Ivoire continued to defend well despite sustained pressure from Senegal, who were reduced to largely speculative efforts from range in what was a frustrating first half from their perspective.
Senegal pressed forward with renewed energy after the interval, and Cisse was involved again as he broke through on goal following some poor defending, only for Boubacar Barry to block his close-range effort with his feet.
Lamouchi's side struggled to get a foothold in the game throughout, and they were continually grateful for Senegal's profligacy, which was showcased agains as Dame N'Doye curled a free kick wide from the edge of the area.
However, 13 minutes from time Giresse's men were offered a lifeline when Drogba pulled down Mane in the area, allowing Sow to step up and convert from the spot.
Senegal failed to create further momentum, though, and they were caught on the counter in the final minute of injury time, Kalou steering home to send the Elephants to their third consecutive World Cup.