Gauff was unhappy her serve was called out after Pliskova hit a missed return and had a long discussion with Pierre Bacchi when told to replay the point.
The 19-year-old American moved on from the second-set exchange and continued her fightback to win 2-6 6-4 6-3.
“It kind of went upward for me from there,” said Gauff.
“I was telling me to stay calm in the next point and not let that be a turning point. Maybe I dragged it out longer than I needed to, but I did what I thought was best in the moment.
“I think it fuelled me.”
Elsewhere in Wednesday’s third-round matches, world number one Iga Swiatek continued her fine form in the Middle East as she beat Ukraine’s Elina Svitolina.
Poland’s Swiatek won the Doha title last week and continued her quest for back-to-back titles with a 6-1 6-4 win over 15th seed Svitolina.
Swiatek, who has won 24 of her past 25 completed singles matches, will face Australian Open runner-up Zheng Qinwen in the quarters.
Gauff’s reward for beating former world number one Pliskova, who had won her 11 previous completed matches, is a quarter-final against Russian Anna Kalinskaya.
