It is a failure and I assume responsibility for it," Lemerre told a press conference after the game.
Tunisia lost top spot in their Group C after the French boss opted to field a second string line-up against the strong Guinean side after securing qualification to the quarter-finals.
Lemerre did not regret the gamble, noting that his Guinea opposite number Patrice Neveu did the same thing but was more successful.
"The result is one thing, the managing of a squad another," said the former France coach. "Guinea did the same thing and they won,” he said.
The former France coach said that his side lost because the Tunisian players lacked spirit.
"The team (Tunisia) lacked character and yes it is a blow.
"At international level players have to be leaders and certain of mine were not tonight (Monday). It is a failure and I assume responsibility for it," Lemerre said.
Neveu, on the other hand, was ecstatic over his side's victory even though he recognizes Tunisia did not field a first string team.
"We are very proud. Perhaps it wasn't their best team but it was still an official international match," he said.
Guinea's victory means they will face the runners-up from Group D on Saturday while holding champions Tunisia will a more uphill task of facing the group winners.