The Lions of Teranga needed just a single point against Colombia to be the only African representative within the knock-out stage.
However, Yerry Mina's late strike broke the hearts of the African nation, as Senegal finished level with Japan on four points and goal difference - but were separated by their disciplinary record.
"This is the law of football. We don't qualify because of fair play, we have a fewer number of points in the fair play but today," he said in the official FIFA press conference.
"I'm proud of my team, their work and today Senegal does not qualify because we don't deserve it. This is life.
"This is one of the rules (fair play). We have a number of rules which are established in the regulations and we have to expect that."
Cisse went on to add that his side were fully aware of the ruling and permutations of their style of play - and tipped them to grow stronger from their Russia 2018 experience.
"We would have preferred to be eliminated in another way, it's a pity for us but this is how it works. We knew these were the regulations but we are fully committed and since we are committed maybe we get more yellow cards, it's a pity.
"I think my players were aware of the regulations but as I said Senegalese players are highly committed so its difficult to play well if you don't play with commitment, I don't know if this regulation is cruel or not but I can't ask my players to go out on the pitch to avoid yellow cards.
"You have to be in contact with other players and it's a shame it worked against us," he added. "I think we did control the match and I'm disappointed for my team and for this generation and these players who fight every single day for our country.
"I will continue to encourage them to be with them because I'm sure we can expect many pleasant things in the future."