Kyrgios was seething with the Brazilian during his last-16 defeat to Italy's Jannik Sinner, calling the match official "horrendous" and "embarrassing" during multiple tirades during the match.
The ATP charged the fiery 26-year-old Aussie with two counts of unsportsmanlike conduct for a total of $10,000, a verbal abuse charge of $20,000 and an audible obscenity violation of $5,000.
Kyrgios, who was hit with a $25,000 penalty for racket abuse and audible obscenity at Indian Wells earlier this month in a match also officiated by Bernardes, stressed at the start of his Miami Open campaign that he was at "peace" with himself on and off the court.
He was, however, incensed with Bernardes' performance and although the Australian was initially upset about the difference in conditions between the main court and Grandstand at the sprawling Hard Rock Stadium, he became enraged with the umpire when his walkie-talkie went off mid-point in the first set.
The pair then became involved in a row which saw a furious Kyrgios docked a point during a tiebreaker and then a whole game at the start of the second set.
"The crowd actually hated him (Bernardes) that much they told him to be quiet," Kyrgios said after his straight-sets defeat.
Kyrgios also complained that the ATP won't do anything to Bernardes.
"The ATP won't do anything about him," Kyrgios said. "He will just show up at the next event and everyone just forgets how bad that was.
"Me, my girlfriend, my team all have to deal with the bad comments and the ATP don't give a (damn)."
Krygios and Aussie partner Thanasi Kokkinakis were set to play in a Thursday doubles semi-final.
