Football manager Steve Alessio said Winderlich is likely to miss at least two weeks with the injury.
"At first we were a little bit fearful that he might have torn it and we know he has had a bit of a history with his hamstring," Alessio told essendonfc.com.au.
"His hamstring is very tight but it is probably the better case scenario for us with regards to Jason.
"It still means, with his history, he will still miss a couple of weeks."
The injury dates back to his knee reconstruction in 2011, when surgeons took a hamstring graft to aid his knee recovery.
He had many hamstring setbacks last year when returning from the reconstruction.
The Bombers could welcome back Michael Hurley to the side on Saturday night against North Melbourne, with the key forward having missed the last two weeks with an ankle injury.
"Hurls has stepped up his training in the last week, he will continue to do that this week and he is probably 60-40 with his approach for this week," Alessio said.
"It all depends on how he pulls up this week but he would definitely be available for the next week."
Hurely's season has been plagued by injuries to his ankle, wrist and concussion.