The Panthers have lost in each of their last eight trips to Pittsburgh.
Each team produced a goal in the second period, but Niskanen put the Penguins in front for good on a slap shot 7:49 into the third.
The winning goal came against Jacob Markstrom, recently called up from the American Hockey League and playing in his ninth NHL game.
The win went to Marc-Andre Fleury, who made 22 saves. It was the 12th victory of the season for the Penguins, most in the Eastern Conference. Florida has lost six out of seven.
Florida's only goal came on a tip-in by Mike Weaver 8:25 into the second period.