The Mexican goal-poacher had been facing two weeks out with a bruised shin after what Ferguson branded a "shocking" tackle by Chelsea defender Ashley Cole in last Sunday's 3-1 win over the London side.
"It's quite surprising, Hernandez trained yesterday," Ferguson told a news conference on Friday.
"He is very lucky. At the time he had no feeling in the leg, there was a numbness there, we thought there may have been some nerve damage... but he's trained very well and he's available for tomorrow."
Hernandez is likely to resume his potent partnership with Wayne Rooney, who has scored in all five of United's league games and notched nine goals including two hat-tricks.
United are the only team still with a 100 percent record in the league, topping the table with 15 points. They are two points ahead of neighbours Manchester City and a further three ahead of Chelsea.
Ferguson expected a tough trip to last year's FA Cup finalists Stoke, who held Chelsea to a 0-0 draw in their opening game of the season.
"The progress Stoke have made over the last few years is phenomenal," Ferguson said. "European football now - who would have thought that a few years ago?
"When you see that Chelsea have gone there and drawn and Liverpool have gone there and lost you can see what a difficult job it is."
