The 24-year-old seamer and hard-hitting batsman has been a regular member of the Indian side in all three formats of the game and has been playing non-stop since the Champions Trophy in England in June.
Pandya was named in India's squad for the first two tests against Sri Lanka and no replacement has been named.
"The all-India senior selection committee in consultation with the Indian team management has decided to rest all-rounder Hardik Pandya for the upcoming test series against Sri Lanka," the BCCI said in a statement.
"Considering Mr Pandya's heavy recent workload, the decision was made to negate any possibility of a major injury concern.
"Pandya will undergo a period of strength and conditioning at the National Cricket Academy in Bengaluru."
Kolkata's Eden Gardens will host the opening match of the three-test series from Thursday with the second and third tests in Nagpur and Delhi.
India will also play three one-day internationals and the same number of T20s against Sri Lanka.
India squad: Virat Kohli (captain), KL Rahul, Murali Vijay, Shikhar Dhawan, Cheteshwar Pujara, Ajinkya Rahane, Rohit Sharma, Wriddhiman Saha (wicketkeeper), Ravichandran Ashwin, Ravindra Jadeja, Kuldeep Yadav, Mohammed Shami, Umesh Yadav, Bhuvaneshwar Kumar, Ishant Sharma
(Reporting by Sudipto Ganguly,; editing by Ed Osmond)
