Shakib fractured his finger during their win over Sri Lanka.
'I know Angelo for a long time since 2006. Yeah, I'm better within the rules', quipped Bangladesh Shakib when asked about the controversy.
After posting a formidable 364 for nine, Reece Topley (4/43) ran through Bangladesh's top order as they could muster only 227 in 48.1 overs.
Matheesha Pathirana bagged four wickets to restrict Bangladesh to 164.
Veteran batter Mahmudullah continues to be out of contention.
Bangladesh needed a new ODI captain after opener Tamim Iqbal stepped aside earlier this month citing a back injury, which would keep him out of the Asia Cup beginning in Multan on August 30.
The Bangladeshi team, whose World Cup campaign begins on October 7 against Afghanistan in Dharamsala, is yet to reveal who will lead the side after Tamim's exit.
The BCB also named a 17-man squad for the Asia Cup that gets underway in the United Arab Emirates on August 27, with batsman Sabbir Rahman and veteran wicketkeeper-batsman Mushfiqur Rahim both returning to the fold.
Chasing Bangladesh's total of 153, Oman could only make 127/9 with Mustafizur Rahman bagging 4/36.
Playing a pivotal role in Scotland's win was Chris Greaves, who followed up his blazing knock with the two important wickets of Shakib Al Hasan (20) and Mushfiqur Rahim (38).