Pavel Kubina scored for the Maple Leafs.
Stafford now has 17 goals on the season, one more than his career high of 16 set last season.
Derek Roy, who plays center on Stafford's line, said the 23-year-old has stepped up offensively since Vanek, who had 32 goals in 54 games, was lost to a broken jaw Feb. 7. Vanek won't return until at least early March.
"He's been making some plays, moving his feet down low," Roy said of Stafford. "He's a strong body in front of the net on the power play and we need that from him. He's playing really well, he had a couple more chances to score some more goals tonight."
Stafford, who narrowly missed scoring a hat trick when a third-period backhander sailed wide, has eight goals in his past 11 games. He started his recent hot streak with a three-goal effort versus the Edmonton Oilers in late January.
"As long as I'm contributing, especially now with Thomas out, we're going to need all the goals we can get and if that's what I'm going to be contributing, than so be it," said Stafford, who was taken 13th overall in the 2004 NHL draft. "I know it's not going to happen every night, but we have a lot of guys in here who can contribute in the goal-scoring department, so I'm just trying to do my part in that aspect as well as trying to be solid everywhere else."
The Sabres played lackluster in a loss to Carolina on Sunday and didn't come out with much energy in this one either.
If not for some great saves by Miller, the Leafs would have had an early lead. The Sabres goalie made a few fantastic saves with his team a man short, sprawling around the crease and keeping out a couple sure Toronto goals.
Miller held the Leafs at bay early with some sprawling saves while Buffalo killed a penalty and the Sabres scored three times in the first against rookie goalie Justin Pogge.
Stafford beat Pogge after John Mitchell's turnover at 12:40 and Paille received a cross-crease pass from Tim Connolly before scoring at 14:19.
Ellis skated out from the corner and managed to slip a weak shot through Pogge at 17:44.
Pogge, making his first start at home, seemed to settle in after that - flashing a glove to take away a wrist shot by Connolly early in the second period. That was one of 13 saves he made during the period.
"That's the truth," said Pogge, who finished with 26 saves. "If it was a playoff race, you wouldn't want to be throwing a young guy in there. I'm happy to be getting a shot at it. I'm just fortunate for the situation."
Kubina made it 3-1 with a power-play goal at 7:28 of the second period.
Stafford scored his second of the night of the season at 7:37 of the third period on a power play.
"The second one was just hanging around the net, being a net rat," Stafford grinned. "It's greasy, but I'll take it."
Toronto intends to keep Pogge around for the rest of their current homestand and may even start him Thursday against Columbus or Saturday against Vancouver.
"This is great for him to go through this," Leafs coach Ron Wilson said. "If it was easy, I'd be worried about him being over-confident. This is going to force him to work harder on his game and that's what he needs to do."
Notes: There have been 138 NHL coaching changes since the Sabres hired Lindy Ruff ... Buffalo is 10-3-1 at Air Canada Centre since the lockout ... Leafs F Jason Blake has 11 goals in his last 14 games for Toronto.