Jol, who has signed a deal until June 2010, will succeed Huub Stevens after his fellow Dutchman takes over at PSV Eindhoven at the end of the current Bundesliga campaign.
Jol's appointment had been widely expected and Hamburg chairman Bernd Hoffmann was delighted to have finally bagged his man. He told the club's official website, www.hsv.de: "We are certain that in Martin Jol we have appointed the right coach."
Jol's assistant will be Zeljko Petrovic, the former coach of Dutch second division side RKC Waalwijk.
Hamburg have been on the look-out for a new boss ever since Stevens announced last November he would be joining Eredivisie champions PSV in the summer.
Jol will be officially presented as Hamburg coach at the start of next week.
The Bundesliga side's sporting director Dietmar Beiersdorfer added: "We are looking forward very much to working with Martin Jol in the future."
Jol joined Tottenham in 2004 after a brief spell as assistant to Jacques Santini and guided them to the brink of Champions League qualification in 2006, only missing out on a top-four finish on the last day of the season.
Hamburg have faded away in the latter part of the Bundesliga season and could even miss out on a UEFA Cup place.
They lie in fifth place, one of four sides on 51 points going into the final game of the campaign.