Italian prosecutors say they will appeal. Only Rudy Guede, 24, has been convicted for Miss Kercher’s murder.
Knox has since left Italy and is on her way back to the US.
She is travelling back to her hometown of Seattle on a commercial flight and is expected to land at around 0100 BST on Wednesday (0000 GMT, 1700 PDT on Tuesday).
Speaking to reporters in Perugia, where his sister was studying at the time of her death, Mr Kercher said: “We accept the decision and respect the court and the Italian justice system.
“We do find we are now left looking at this again and thinking how a decision that was so certain two years ago has been so emphatically overturned, which raises other questions.
Speaking after an Italian court cleared Amanda Knox and Raffaele Sollecito of murder, Meredith’s brother Lyle said it felt like it was “back to square one”.
Their mother, Arline, said: “What happened to my daughter, Meredith, is every parent’s nightmare.
“Of something so terrible happening, when basically she was in the safest place, her bedroom.”
Prosecutors said Miss Kercher was killed in a brutal sex game which went wrong.
Mrs Kercher admitted she could appreciate why Knox would feel she had lost her life over the last few years.
“I don’t think anyone’s going to get off scot-free,” she said. “Their lives have been disrupted – no-one is untouched by this.”
Earlier, UK Prime Minister David Cameron said he felt sympathy for the Kerchers.
“They previously had an explanation about what happened to their daughter and they don’t have that any more, and I think all of us should be thinking of them,” he said.