Huberdeau scored the only goal in the shootout and Ellis, making his second start because of the injuries to Roberto Luongo and Al Montoya, stopped Frans Nielsen, John Tavares and Josh Bailey to help the Panthers to a 4-3 win at BB&T Center.
Ellis, acquired in a trade with the Dallas Stars last March, won for the first time in seven games with the Panthers. His first start of the season resulted in a 4-3 shootout loss against the Dallas Stars on Thursday.
Ellis was 0-5-0 with a 4.81 goals-against average and .836 save percentage in six games with the Panthers last season.
"It's just nice to be able to win," said Ellis, who made 25 saves. "I mean, it's taken me seven games to be able to do that, to contribute at all. Last year I wasn't the goalie that I wanted to be for this team. I stepped into a great situation here where I've had a chance to play. I got to play a lot down in San Antonio (of the American Hockey League) and I just want to contribute any way I can. It's nice to be able to get three points so far."
The Panthers had lost six of their past seven shootouts and are 7-10 on the season.
"Ellis played great," center Nick Bjugstad said. "Big shootout win. We haven't won very many shootouts lately. It's good to have Ellis come in here and step up and Huberdeau get a good shootout goal."
The Islanders are 7-3 in shootouts. Nielsen was 5-for-9 in shootout attempts and Tavares scored against Ellis on a breakaway in the second period.
Asked whether he was happy to get another chance in the shootout to stop Tavares 1-on-1, Ellis said, laughing, "Yes and no. I didn't want to be embarrassed again. When you're playing against one of the top players in the world, one of the best shootout guys in the League, patience is the key and you just try to get something on it. He beat my stick, but I was able to get my knee down and get on the top of my pad."
Before his shootout goal, Huberdeau had a spectacular goal in the third period, his second in two games after an 18-game drought.
Huberdeau broke a 2-2 tie at 9:26 of the third period with a spectacular goal. He took a pass from Aleksander Barkov down the left wing, skated toward the middle of the ice, then did a 360-degree turn before sending a shot along the ice off the left post.
"I don't know why I did that," Huberdeau said. "Instead of going right at it and try to shoot it, I did a little spin. Maybe the goalie doesn't expect it. I was hoping it was going to stay 3-2 the whole game to win in regulation, but they came back again and we found a way to get the two points."
Erik Gudbranson and Bjugstad scored for the Panthers (29-23-14), who are two points behind the Boston Bruins for the second wild-card spot in the Eastern Conference.
The Panthers won despite giving up the lead three times.
"It just shows we can play with anyone when we want to," Bjugstad said. "But it comes down to us showing up and playing as hard as we can and limiting the turnovers. We played well tonight, pretty well. If we can keep that going, we proved we can play with these guys, why not anyone? We've got to keep it going."
Gudbranson, fellow defenseman Willie Mitchell and Jaromir Jagr all missed the shootout loss against Dallas because of the flu. They returned against New York, but rookie defenseman Aaron Ekblad and forward Tomas Kopecky were out because of the illness.
Mitchell returned after missing 16 games, the first 15 because of an upper-body injury.
Tavares, who began the day in a four-way tie for the NHL scoring lead, scored his career-high 32nd goal and had two assists. Nick Leddy and Bailey scored for the Islanders (42-21-4).
"I thought we had some pretty good chances," Tavares said. "It was just one of those games it was just slower and you could see pucks were bouncing quite a bit. It was just a tough night to really generate much through the neutral zone, but we created some chances on the forecheck and in the zone and got a big PP goal as well."
Michal Neuvirth, acquired from the Buffalo Sabres at the NHL Trade Deadline on Monday, made 15 saves in his Islanders debut. His last start for Buffalo came against the Panthers when he faced 46 shots in a 5-3 loss at BB&T Center on Feb. 28.
"Totally different game, very tough mentally," Neuvirth said. "[I] just couldn't get into the game and into my rhythm. It was a tough game to play."
The Islanders extended their lead to three points atop the Metropolitan Division over the New York Rangers, although they have played four more games.
Bailey made it 3-3 at 12:48 of the third with a one-timer off Tavares' backhand feed that beat Ellis high to the glove side.
Gudbranson, who hadn't scored since Feb. 3 against the Islanders, ended his drought Saturday with the only goal in the first period. His low wrist shot from the point appeared to bounce off the skate of Islanders forward Casey Cizikas and trickled through Neuvirth's pads.
Tavares, who scored 31 goals in 2011-12, tied the game on a breakaway at 4:39 of the second period after Anders Lee tipped a cross-ice pass in the neutral zone. Tavares beat Ellis with a backhand after a series of quick dekes. Lee extended his point streak to four games (two goals, two assists).
Bjugstad, whose errant pass led to Tavares' goal, gave Florida the lead again at 8:20 with a high backhand from close range after taking a slick pass from Jussi Jokinen.
"It was kind of an embarrassing pass by myself," Bjugstad said. "I whiffed on it. You can't do that when you're the last guy back with Tavares especially. I tried to keep my head straight. Obviously you're frustrated. I had to make sure I kept my head up. We kept going is what happened. I kind of cost us a goal there. We might not even be in the shootout if I don't do that, but we responded well."
The Panthers took two of three in the season series; they won 4-2 at Nassau Coliseum on Feb. 3 after losing 4-3 in a shootout at BB&T Center on Nov. 14.
Florida is 3-2-1 on a season-long seven-game homestand that ends against the Winnipeg Jets on Thursday when Luongo could return from his shoulder injury.
"I was happy," Panthers coach Gerard Gallant said. "A total performance from 20 guys that battled hard and that's how it's going to have to be. We've got 16 games left and we have to play hard, compete hard, and get a chance to win.
"[We've got] some days off, we still have a few guys with the flu. It gives us time to get back and hopefully get everybody healthy for Thursday. Willie coming back is real big for our team, we're hoping for (Luongo) on Thursday. A perfect time for the break."