Early in the 2008–09 season, the Penguins and Red Wings met for the first time since the Stanley Cup series on November 11, 2008. With the Penguins down by three goals in the third period, Staal notched his second career NHL hat trick to tie the game, then set up Ruslan Fedotenko's overtime winner to defeat the Red Wings 7–6. On December 2, 2008, he was named to the rotating position of alternate captain for the Penguins for the month of December. The following month, on January 8, 2009, the Penguins announced that they had extended Staal's contract through the 2012–13 season. Terms of the contract were for $16 million, payable as $3.5 million for the first two seasons, and then $4.5 million for the last two years, resulting in a $4 million salary cap hit. He completed the season bouncing back from the decreased production of his sophomore year with a career-high 27 assists and 49 points. On June 12, 2009, Staal and the Penguins won the Stanley Cup when they defeated the Detroit Red Wings 2–1 at the Joe Louis Arena. Staal had two goals and an assist in the seven-game series, and scored a shorthanded goal that was a pivotal point in Game 4 of the series.