The Lions managed to secure a fourth successive season in the Championship and also reached the FA Cup semi-final at Wembley.
Shittu, named captain in the absence of the injured Paul Robinson, has been a rock at the heart of Kenny Jackett's defence and collected his Player of the Year award on Sunday night.
He said: "I was shocked to get the captain's armband, but it has been a dream come true for me since I came back to Millwall.
"I want to thank everybody - my team-mates, the gaffer, the chairman and directors and everyone who works behind the scenes at the club.
"There have been a lot of things that have happened this season that I'll remember forever.
"We're proud to stand here and say that we are still in the Championship for another year and have been to Wembley."