Wood had returned figures of 0-29 from eight overs before going off the field shortly before tea on Thursday at Lilac Hill.
The 35-year-old was playing his first match since having knee surgery in March and will now undergo precautionary scans on his left hamstring.
Although England's medical team is confident the niggle isn't serious, the fact Wood hasn't been able to get through the three-day match without an injury scare bodes poorly for his chances of being available for the first Test, starting on November 21.
"He has some stiffness in his hamstring, which has kept him off the field for some time during the second session of the first day and will undergo a precautionary scan tomorrow," England said in a statement.
"He is expected to bowl again in two days' time. It is unlikely he will return to the field today."
The news was much better concerning Stokes and express paceman Jofra Archer, both of whom have been under fitness clouds.
Stokes, playing his first match since injuring his shoulder in July, took 6-52 off 16 overs as the Lions posted 382 from 79.3 overs on a batter-friendly wicket.
The injury-plagued Archer, who has played just two Tests over the past four years, finished with 1-51 off 12.3 overs.
The return of Stokes to the bowling crease would be a huge relief to an England side needing the star allrounder firing on all cylinders if they are to be a chance of upsetting Australia.
But England batsman Harry Brook was feeling for Wood, who is England's most experienced paceman but has endured some rotten luck on the injury front.
"That's not ideal is it," Brook said of Wood's hamstring niggle.
"But that's part of being an extremely fast bowler."
England named a full-strength XI for the warm-up match, but interestingly selected spinner Shoaib Bashir as part of the England Lions side.
The 22-year-old has played 19 Tests, including three of the five in England's recent 2-2 series draw with India.
But his omission from the main England side for the warm-up match could indicate the visitors are unlikely to select him on the pace-friendly Optus Stadium wicket, with Joe Root's part-time spin an alternative option.
Root was pummelled on Thursday, finishing with 1-117 off 14 overs.
Archer, Wood, Gus Atkinson and Josh Tongue were named as part of a four-pronged pace attack for the warm-up match, with Stokes adding further firepower.
Will Jacks (84 off 85 balls), Ben McKinney (67), 17-year-old Thomas Rew (55), Jordan Cox (53) and Matthew Potts (53) all posted half-centuries.
Right-arm quick Brydon Carse was unwell on Thursday and stayed at the team hotel.
