The 36-year-old right-hander achieved the milestone during the fourth day of the third and final Test against Pakistan in Sharjah.
The former captain is the first Sri Lanka to aggregate 11,000 runs. The list for most runs in Tests is headed by former India batsman Sachin Tendulkar.
Tendulkar, who retired in November last year, has scored 15,921 runs in 200 Tests.
Jayawardene scored 46 on Sunday and currently has 11,033 runs in 141 matches.
List of players with 11,000 or more runs in Test cricket
Sachin Tendulkar (India) - 15,921 runs (200 Tests)
Ricky Ponting (Australia) - 13,378 (168)
Jacques Kallis (South Africa) - 13,289 (166)
Rahul Dravid (India) - 13,288 (164)
Brian Lara (West Indies) - 11,953 (131)
Shivnarine Chanderpaul (West Indies) - 11,229 (152)
Allan Border (Australia) - 11,174 (156)
Mahela Jayawardene (Sri Lanka) - 11,033 (141)