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Josh Scobee thought that he had opened the scoring early in the first half, but the kicker's 47-yard effort was chalked off for a holding penalty by the home side.
The quarterback got Jacksonville back into a strong field position, but a mis-timed snap saw the ball come loose, leaving Scobee with another kick.
Bortles threw another interception early in the third quarter, with Brent Grimes making the play for the Dolphins to increase the AFC East side's lead.
The Jaguars did not give up, with Bortles managing a deep pass to Allen Robinson in the final minutes to cut the Dolphins' advantage, but it was not enough for the hosts to avoid their seventh defeat of the season.
The result leaves the Dolphins third in their division with a 4-3 record, while the Jaguars remain bottom in the AFC South.