Chasing a ball towards the boundary in the 37th over, Lyon pulled up and was immediately in pain and appeared to know he was in trouble. He hobbled to the edge of the field where the physio began to assess him then had to be helped around the rope to the pavilion.
A CA spokesperson said Lyon would be further assessed overnight but there were no immediate plans to send him for a scan.
Lyon had already shaped as a significant figure in this match - as he was at Edgbaston - having removed Zak Crawley to break an opening stand of 91, drawing him down the pitch for a stumping that was expertly completed by Alex Carey.
Ben Duckett, who led England's batting effort on the second day, expected Lyon to play a key role and questioned the impact his absence would have on the rest of the attack after the quicks opted for a short-ball approach.
"It's a huge shame and I really hope it's not too bad for him," he said. "You never want to see anyone go down with an injury. We all wish him the best. He was going to play a massive part in that fourth innings, he's such a good bowler. It will be interesting to see how they go about it.
"If they keep going bumpers with all four bowlers, I think they'll be quite tired by the end of it, especially with back to back Tests. Travis [Head] bowled all right tonight, so he maybe he will bowl a bit."
Should he not be able to play any further role in this game it would leave Australia a specialist bowler down and needing to turn to Smith, Travis Head and Marnus Labuschagne for any spin.
It would appear that for the second time in consecutive Lord's Tests Australia have suffered a major blow after Smith was concussed in 2019. On that occasion he was able to replaced under the protocols by Labuschagne, but this time the team will have make do.
"He [Murphy] has been bowling beautifully in the nets and bowled really well in India when he got his opportunity as well," Smith said. "I'd be confident if he came in he'd do a terrific job for us, but fingers crossed Nathan's all right."
Legspinner Mitchell Swepson is now also in the UK having recently signed to play the County Championship for Glamorgan.