Atapattu, who has been out of action since March following surgery to repair a disk problem in his lower back, is not expected to return till the Champions Trophy in India in October.
Jayawardena, Sri Lanka's captain on the recent tour of England, will lead in two home Tests against South Africa starting later this month and a tri-series also featuring India in August, De Mel said on Monday.
"Marvan needs time to rehabilitate and strengthen his back," the chief selector told reporters.
"He was very eager to get back on the field but we do not want to rush him into the team until he is 100 percent fit. He should be back for the Champions Trophy."
Jayawardena earned praise for his leadership on the England tour where his team fought back to draw the Test series 1-1 and blanked the hosts 5-0 in the one-dayers.
South Africa, who arrive in Sri Lanka later this week, will play the first Test at the Sinhalese Sports Club ground in Colombo from July 27. The second Test will be held at the Sara stadium, also in Colombo, from August 4.
The tri-series between Sri Lanka, South Africa and India will be played in Colombo from August 14-29.