The Sri Lanka captain got two suspension points and was fined 100 per cent of his match fee.
Hales made 147 and Bairstow 139 as England surpassed their own previous all-time record ODI total of 444 for three.
A back spasm shortly before Sunday's toss meant Morgan missed England's 38-run win over world champions Australia as his side went 2-0 up in a five-match series.
Mustafizur was yet to regain his fitness from the injury which also forced him to miss the recent three-match Twenty20 series against Afghanistan.
Brathwaite’s unbeaten 59, rain, and deteriorating light eliminated the Sri Lankans’ chances of levelling the series.
England lead the five game series with Australia 2-0 with three matches remaining.
Match officials charged Chandimal after TV footage from the final session's play on Friday appeared to show the captain taking sweets out from his left pocket.
Overall, it also represented a 13th loss from their last 15 matches at this level that have produced a result.
Australia suffered a seventh defeat in their last eight ODI matches.
The most Australia have ever made batting second to win an ODI is the 334 for eight against England at Sydney in 2011.
Umpires Aleem Dar and Ian Gould had raised concerns about the condition of the ball nearing the end of the second day.
Warner has already agreed deals to play in lower-level Australian grade cricket and at a tournament in Canada in July.
Afghanistan captain Asghar Stanikzai said he was surprised by the margin of defeat but insisted the team with their new glowing red Test caps would "learn lessons" from the loss.
Ravindra Jadeja took four wickets to help skittle out Afghanistan for 103 in the final session while following on.
"I am of the view that it (the invitation) is an insincere, cunning move, to use us when the cricket administration is in such a deplorable state."
