Tamim, who is Bangladesh's leading run-getter across formats, registered scores of 0, 19 and 2 in the three games prolonging his patch of bad form.
"I think the important thing for him now is to take some rest, recover well, feel fresh and come back strongly. I am sure he will do this," Shakib suggested regarding Tamim.
Tamim's poor show in the Sri Lanka series follows a disappointing World Cup campaign in England and Wales where he managed 235 runs at a paltry average of 29.37 in eight innings.
Tamim's failure to score freely at the showpiece event was thought as one of the reasons why Bangladesh could not live up to the expectations and finished at eighth in the ten-team table by the conclusion of the tournament.
The onus was further placed on Tamim during the Sri Lanka series as they were missing the services of Liton Das and Mohammad Saifuddin but his sum of 21 runs in three innings did little to help Bangladesh's cause.
"There are a lot of negatives. We have to hold it tight and come back strong," Tamim had said after his side's 122-run loss in the final match.
Shakib declared the team management needed to focus on adopting a clear rotation policy in order to keep players fit and fresh for longer periods of time.
He is expected to return to the cricket action in next month's home series versus Afghanistan.
"It's not possible for a player to play when he feels stretched. So these breaks are important. These breaks also create opportunity for others," said Shakib.
"I can give you the example of India. Last year there were fewer injuries to players. One reason is they played with a rotation policy," he added.
Afghanistan's tour to Bangladesh will include a one-off Test match in addition to the Twenty20 series that originally involved Zimbabwe.