Wildcard Barty's 6-4, 5-7, 6-3 win sets up an all-Australian clash in the second round of the WTA hardcourt event against 14th seed Samantha Stosur.
But for the 23-year-old Bouchard, a former world number five who has slumped to 56th in the rankings, it was another blow after her first-round exit in Indian Wells.
"It has been a bit of a struggle," said a stone-faced Bouchard, who was unable to account for her loss of form.
Barty reproduced the gutsy tennis that helped her secure her maiden WTA title at the Malaysian Open in Kuala Lumpur last month.
"We've had a good pre-season and get a good foundation and the stars aligned a bit for us this year so far. We have worked hard and it is just that hard work starting to pay off," said the Australian.
The 20-year-old, who took time out from tennis in 2014 to play cricket, has never come up against her compatriot Stosur before and while she will start as clear underdog, she is relishing the challenge.
Serbia's Jelena Jankovic was another high-profile early exit, the 2008 Miami finalist falling 4-6, 6-4, 7-6 (7/3) to Kazakhstan's Yaroslava Shvedova.
Local favorite and Rio Olympic gold medalist Monica Puig was comfortably dealt with 6-2, 6-4 by Romanian Sorana Cirstea.
The Puerto Rican Miami-resident struggled from the outset and although she battled back well in the second set, Cirstea kept her cool to book a second round meeting with Latvian 19th seed Anastasija Sevastova.
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