Tendulkar was taken by surprise when stand-in captain Rahul Dravid declared the first innings closed at 675 for five as he was just six runs short of his second successive double-century.
"It's a mistake made by the team," Ganguly was quoted as saying by the Press Trust of India news agency.
"There is no point making it an issue," said the Indian skipper, who returned home for treatment after missing the opening Test due to a back injury.
Dravid was named captain in Ganguly's absence, eventually leading India to their maiden Test triumph in Pakistan on Thursday. The tourists won the match by an innings and 52 runs.
"Whoever has made a mistake, it's for the team to accept it. It's for all of us to accept it, so let's not make it an issue," said Ganguly.
"Whether it's Sachin, Rahul, myself or whoever has made a mistake let's forget about it and go ahead and win the series. We are friends. As friends, we have made mistakes. As friends, we forgive each other."
However, former Australian captain Ian Chappell, writing in the Hindustan Times, said Dravid had established the team priority by declaring when he did.
"This was the correct decision as it showed his team, a blending of youth and experience, that victory rather than personal milestones is the ultimate prize," Chappell said.
Ganguly said he hoped to be fit for the third and final Test starting at Rawalpindi on April 13.
"I am looking forward to the third Test. I hope to be fit in the next few days and join the squad," he said.