Jordan Veretout stood over the penalty for a full three minutes, but he never got the chance to take it after the referee signalled an intervention from the video assistant referee, and awarded a free-kick to the visiting team for an offside infringement.
Higuain - the scorer of a hat-trick last weekend - sealed the win four minutes from time with his 14th Serie A goal this season and 50th for Juventus.
Since losing 3-2 to Sampdoria on 19 November, Juve have recorded 15 shutouts in all competitions - including clean sheets against Barcelona, Napoli, Inter and Roma.
But there was an incident in the first half that took centre stage.
With four goals in six league starts so far this season, the Italian global is doing his best to make it hard for Juventus head coach Massimiliano Allegri to leave him out of the playing XI.
"Did I understand the referee's decision? The wait was long and luckily the penalty was taken away, I thought there was a foul on the action before but then many other things are seen on TV", continued Allegri.
"Now we have to recover for the Champions League". I've always been grateful to Fiorentina, and always will, for the way they looked after me and helped me develop, but I made a career choice and now I play for another team. Bernardeschi, a product of Fiorentina's youth system, was playing his first match in Florence after joining record Serie A champions Juventus for around $45 million.