Tyler Kennedy, Chris Kunitz and Max Talbot scored for Pittsburgh, which has won four consecutive and seven of eight - all without captain Sidney Crosby (concussion). The Penguins have also been without All-Star center Evgeni Malkin (sinus infection) for five games.
Marc-Andre Fleury stopped 29 New York shots in a 1-0 win on Jan. 25, the Penguins' 10th consecutive home victory against the Islanders.
Johnson, making his third start since Dec. 22, fell just short of his second shutout this season, when he fought Islanders goalie Rick DiPietro in the final minute.
The Islanders have lost six of eight and haven't won in Pittsburgh since Dec. 21, 2007.
It didn't matter that the Penguins were missing their two biggest stars again, or that they beat the Rangers in New York in a shootout on Tuesday night.
Malkin has been practicing recently and is expected to return soon. There is no timetable for Crosby to rejoin the lineup. The Penguins lost another center, Mark Letestu, who injured a knee during Tuesday's morning skate in New York.
Pittsburgh received some good news Wednesday when the NHL rescinded an automatic one-game suspension for center Jordan Staal, who was ejected Tuesday night after he delivered a gloved punch to the head of Rangers forward Brandon Prust.
Kennedy scored his ninth goal and first since Jan. 12 8:08 in when the rebound of Paul Martin's shot from the left point squirted to him on the right side. Kennedy's shot from a bad angle near the boards near the bottom of the circle beat DiPietro.
The Islanders have allowed the first goal in 13 of 14 games and are 5-25-4 in games in which they trailed 1-0.
New York's deficit doubled five minutes later when Kunitz scored for the fifth time in eight games. He let go a backhander as he drove to the net down the right wing, and the shot appeared to handcuff DiPietro and get past him.
Kunitz has 10 goals since Dec. 23 and 18 on the season, the most he has scored since the 2007-08. He is seven shy of his career high.
Talbot added an empty-net goal in the final minute for his 100th career NHL point.
One of Johnson's best saves came midway through the third when he gloved a slap shot from the left point off the stick of Travis Hamonic. He also stopped Jack Hillen from in close in the final period.
Notes: Johnson and DiPietro fought in the Islanders' end with 16.5 seconds left. ... The Penguins are 17-2-2 against the Islanders at home in the past 21 meetings and 13-1-2 in the last 16 overall. ... There have been 11 total goals in the four games these teams have played this season. ... Martin had two assists.