However, the association's anti-doping tribunal found that only a limited degree of fault could be attributed to Don, who was crowned world champion in Switzerland last month and has this year undergone nine other drugs tests that all tested negative.
But the suspension means that Don will be automatically banned from competing in future Olympic Games under the byelaws of the British Olympic Association, which issues life suspensions to drug offenders representing their country.
"The tribunal does not believe that Tim Don had any intent to take any prohibited substance, nor that Don has ever attempted or had the intent of avoiding the rules relating to whereabouts testing," it said.
The tribunal ruled Don, 28, ineligible to take part in competition for a period of three months running from September 27.
It also "considered that there were inconsistencies and inadequacies in the existing (testing) system, giving rise to confusion which is not in the interests of athletes, the BTA or UK Sport."
Happier times for the champ
Don, long considered an advocate of drug-free sport throughout his career, said: "I have never taken, or even considered taking, a performance-enhancing drug in my life, and I am absolutely devastated to receive a suspension for contravening anti-doping regulations.
"I fully understand that it is my responsibility as a professional athlete to log my whereabouts on the UK Sport system and accept that it is due to my forgetfulness and lack of understanding of the online system following its launch last year that I have received this ban.
"I am clean"
"However, I am a clean athlete who has been tested for drugs on nine separate occasions this year with no adverse findings, and the tribunal and British Triathlon acknowledge there is no way I was deliberately trying to miss a test."
Don offered a full explanation into how he had missed the tests.
"On two occasions I was travelling overseas to represent Britain in international competition and failed to amend my location details.
"On the third occasion I went to an athletics competition in Loughborough which ran late. I arrived back home later than intended and minutes after the one hour window that is given for testing had expired."
Don, who finished out of the medals at the Commonwealth Games in March but was considered a firm gold medal hope for the 2008 Olympics in Beijing, is the latest big name in British sport to fall foul of the 'three-hits' rule with regard to drug testing.
The announcement comes just over a month since Commonwealth 400 metres champion Christine Ohuruogu was suspended.
Ohuruogu was handed a one-year ban and will also miss any future Olympic Games.