Tootle has made 145 appearances for the Railwaymen in all competitions, scoring twice while operating across a number of positions.
The 22-year-old has adapted seamlessly to life in npower League One this season, making the left-back slot his own.
Alex boss Steve Davis told the club's official website: "I am very pleased that he wanted to stay with us and that he wants to remain here for the foreseeable future.
"You want to try to keep the nucleus of the squad together, the backbone in place. It is great for both parties."
Harry Davis, the manager's son, joined Tootle in committing his future to Crewe on Monday afternoon.
Along with Tootle, the 21-year-old is a graduate of the club's famous youth academy and has played 84 games, scoring five times.
Both players started Saturday's 1-0 victory over Scunthorpe.