The eighth seed - a quarter-finalist at Flushing Meadows in 2012 - succumbed to a 7-5 6-4 loss against the world number 42.
Ivanovic made the initial break of serve in the first set, but soon found herself on the back foot as Pliskova broke back in the fifth game and proceeded to move into a 4-3 lead.
But former number one Ivanovic refused to go down without a fight - winning the eighth on her opponent's serve to level matters.
However, Czech Pliskova claimed one more break of serve in the opening set to leave herself serving for the lead, which she did with ease.
The second set proved to be another tight affair, but the cracks began to show for Ivanovic in the sixth game when she had to survive two break points to remain level with Pliskova.
But that proved to be her final game win on her own serve, with Pliskova - despite dropping a service game of her own - holding on to win the match.
While Pliskova can revel in her best grand slam performance to date, Ivanovic will be left to rue 29 unforced errors that contributed to her defeat.
Pliskova will meet 29th seed Casey Dellacqua of Australia in the third round.