Shittu's previous deal was set to expire next month but the 32-year-old centre-back, who captained the Lions for most of the season in the absence of the injured Paul Robinson, has committed himself to The Den until 2015.
He believes the future is bright at the club despite manager Kenny Jackett's shock resignation last week.
"There's been a couple of months of talks and I'm delighted to have got it done," he told the club's official website.
"We have had a lot of ups and for me to be staying here shows that I believe in this club and I believe a lot can come from it."
Millwall chief executive Andy Ambler added: "We're delighted that Danny has committed himself to the club for another two years.
"We were keen to ensure that the foundations Kenny Jackett has put in place would be available for the new manager to build on and Danny was a key element of that."