The Sharks appeared to take a 4-3 lead 51 seconds into the second period, but the goal was nullified for goaltender interference on Couture, who was given a two-minute penalty.
"I didn't have much of a view," Fleury said. "I was looking at the puck and couldn't look to my right. The ref made the right call."
Couture did not agree.
"I haven't seen the replay yet but I thought I was outside of the crease," Couture said. "I thought Fleury kind of ran into me, but I'll have to look at it. Tough way to lose."
Stone scored on the ensuing power play at 1:31 to give Vegas a 4-3 lead.
Karlsson scored shorthanded at 7:35 of the third period for the 5-3 final.
Eakin gave the Golden Knights a 1-0 lead 58 seconds into the first period. Miller scored shorthanded at 4:37 to make it 2-0, and Pacioretty extended the lead to 3-0 at 6:11.
"We were down 3-0 [6:11] in," Sharks coach Peter DeBoer said of pulling Jones. "I didn't put it on [Jones]. We needed a shot in the arm to change our momentum."
San Jose scored three goals in 2:09 to tie it. Couture scored 4-on-4 at 16:59 to make it 3-1, Hertl scored a power-play goal 39 seconds later to make it 3-2 at 17:38, and Thornton tied it 3-3 at 19:08.
"I don't think the intermission could've come at a better time,"said Stone, whose three goals lead the NHL. "To be able to get in the locker room, control our emotions a little bit, get out there and get back to what we do, no matter how you get there, the game is still tied in the first period on the road. Yeah, we gave up a three-goal lead, but we're still in a good spot."
The Sharks became the first team in Stanley Cup Playoff history to tie a game in the first period after trailing 3-0.
San Jose was 1-for-8 on the power play after going 1-for-5 in Game 1. Vegas is 2-for-7 in the series.
"Special teams were the difference," DeBoer said. "It's hard to win this time of year if you don't win the special teams. When you give up the first three goals of the game and lose that battle you're playing with fire. That was disappointing."