After the 2012 season, Scutaro and the Giants agreed to a 3-year, $20 million contract which became official on December 7, 2012. In 2013, Scutaro was the starting second baseman, with Tony Abreu and Nick Noonan as his main backups. In 81 games in the first half, Scutaro hit .316/.367/.400 with 2 HR, 22 RBI and 37 R, and he was named to the 2013 MLB All-Star Game. Scutaro played his last game of 2013 on September 15, and was officially shut down on September 24. He underwent surgery on September 27 that inserted a pin in his left pinkie correcting his mallet finger, an injury he suffered on June 11 against the Pirates when he was hit by Tony Watson. In 127 games in 2013, he hit .297/.357/.369 with 2 HR, 31 RBI and 57 R.