Levy was appointed as Spurs chairman in 2001 and departs after the club won last season's Europa League to end a 17-year trophy drought.
"I am incredibly proud of the work I have done together with the executive team and all our employees," Levy said in an official statement. "We have built this club into a global heavyweight competing at the highest level.
"More than that, we have built a community. I was lucky enough to work with some of the greatest people in this sport, from the team at Lilywhite House and Hotspur Way to all the players and managers over the years.
"I wish to thank all the fans that have supported me over the years. It hasn't always been an easy journey but significant progress has been made. I will continue to support this club passionately."
Levy was the longest-serving chairman in the Premier League and moved Tottenham towards regular European competition.
The 63-year-old played a significant role in developing the club's training ground and the building of a brand new stadium, which came at a reported £1.2 billion cost.
However, his tenure in north London has been a rocky one, with supporters often frustrated by the club's transfer operation under his leadership.
Spurs had only won the 2008 EFL Cup under Levy until May, when Ange Postecoglou led the side to victory in the Europa League final in Bilbao.
It came with Spurs finishing 17th in the Premier League and led to Levy dismissing Postecoglou and replacing him with Thomas Frank, still leaving many dissatisfied.
Tottenham also confirmed that Peter Charrington will step into the newly created role of non-executive chairman as part of an ambition to "deliver long-term sporting success".
He said: "I am very honoured to become non-executive chairman of this extraordinary club and, on behalf of the board, I would like to thank Daniel and his family for their commitment and loyalty to the club over so many years.
"This is a new era of leadership for the club, on and off the pitch. I do recognise there has been a lot of change in recent months as we put in place new foundations for the future. We are now fully focused on stability and empowering our talented people across the club, led by Vinai (Venkatesham) and his executive team."