Shakib last played a Test when Bangladesh took on Pakistan in Mirpur in December 2021.
The KKR pacer surpassed Shahid Afridi's record of 39 wickets in the biggest stage of the shortest format of the game.
Captain Dasun Shanaka announced on Saturday that Theekshana will be kept away from Sunday's match.
The incident took place in the 11th over of the match when Mehedy Hasan was bowling while Danushka Gunathilaka at the non-striker's end.
Iqbal also pointed out that the pitch was two-paced.
Hours before the start of the first ODI against Bangladesh, two Sri Lanka players and one coach tested positive for Covid-19.
Bangladesh has announced the squad for the first two ODIs which will be played on Sunday (May 23) and May 25 respectively.
Bangladesh captain Tamim Iqbal pleaded guilty to the offence after the match.
For Sri Lanka, the fast bowling pair of Nuwan Pradeep and Lahiru Kumara take the places of Kasun Rajitha and Isuru Udana.
The ongoing World Cup has been hit by the rain and there is a possibility more games will be affected due to the bad weather.