The 35-year-old cricketer limped off the field slowly and sat down for a few minutes as a member of Australia’s medical team assessed his injury.
Lyon appeared emotional, wiping away tears, and eventually made his way towards the dressing room, aided by a staff member who provided support to prevent any balance issues.
The extent of Lyon’s injury and the impact it may have on his further participation in the Test match or the series remains uncertain.
“Nathan Lyon suffered an injury to his right calf while fielding in the final session today,” a Cricket Australia spokesman said.
“He will be further assessed after play. A further update, if available, will be shared in the morning.”
Lyon’s absence from the rest of the second day and potentially much longer is a huge setback for Australia’s bid to retain the Ashes.
Pat Cummins‘ side lead 1-0 after winning the first Test of the five-match series at Edgbaston.
Earlier on Thursday, Lyon had dismissed Zak Crawley to claim his 496th Test wicket and ninth of the series.
Lyon’s appearance at Lord’s made him only the sixth man to play in 100 consecutive Tests and the third Australian after Allan Border and Mark Waugh.
His 496 Test wickets place him eighth on the all-time list and fourth among spinners.
Shane Warne and Glenn McGrath are the only Australians to have taken more Test wickets than Lyon.
(With AFP inputs)