Speaking at Home Office questions in the Commons, Theresa May said: "He has experienced the service evolving over the years and as Director General has lead the service through particularly challenging times of change and unrest, including the aftermath of the 7/7 bombings.
"His tireless work helped ensure the delivery of a safe and successful Olympic and Paralympic Games last year.
"I commend and thank him for his invaluable contribution to public safety and national security."
Shadow Home Secretary Yvette Cooper said: "We also give thanks for the work Sir Jonathan Evans has done over many years for the security of this country."
Outgoing MI5 chief Jonathan Evans was appointed a Knight Commander of the Order of the Bath in January after a long career dedicated to fighting terrorism.
The Security Service director general took the top job almost six years ago at a time of unprecedented public focus on the agency in the wake the 9/11 attacks in the United States and the July 7th Tube bombings in London in 2005.
Sir Jonathan said at the time: "It's a privilege to lead MI5 and I view this honour as a recognition of the significant contribution by the men and women of the Security Service in securing the Olympics this year and the country every year."