The 25-year-old went into the penultimate event holding a 113-point lead and looked set to stay in contention after throwing a personal best (42.16m) in her weakest discipline, only for Thiam to respond with a brilliant 57.91m.
Johnson-Thompson had too much to do in the final event, the 800m, and fell short by 57 points as Thiam again triumphed on the big stage.
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But it was a fine championships from the Brit, who ended up with a personal-best score after she finished first in the third heptathlon 800m heat in a season's best of 2:09.84 to secure the silver.
Thiam clocked 2:19.35 in the final two-lap event but it was enough for her to close out the gold and leave Johnson-Thompson to take second place.
Nafissatou Thiam of Belgium celebrates after winning Gold in the Women's Heptathlon during day four of the 24th European Athletics Championships at Olympiastadion
Image credit: Getty Images
However, the Commonwealth champion can take great heart from a championship that has produced more highs than lows.
She posted season’s bests in all four events on day one – the 100m hurdles (13.34 secs), high jump (1.91m), shot (13.09m) and 200m (22.88s) – to lead going into Friday.
Johnson-Thompson increased that advantage in the long jump (6.88m), but was again left ruing her inability to compete in the javelin as Thiam secured a 305-point swing.
In the end, the remarkable Thiam had enough to secure the gold medal once again with the second-best score of her career and her best ever at a major championship.
KJT v THIAM EVENT ONE: 100m hurdles
Johnson-Thompson: 13.34 seconds, 1074 points (4th)
Thiam: 13.69 seconds, 1023 points (14th)
EVENT TWO: High jump
Johnson-Thompson: 1.91m, 2193 points (1st)
Thiam: 1.91m, 2142 points (2nd)
EVENT THREE: Shot
Thiam: 15:35m, 3026 points (1st)
Johnson-Thompson: 13.09m, 2926 points (2nd)
EVENT FOUR: 200m
Johnson-Thompson: 22:88s, 4017 points (1st)
Thiam: 24.81s, 3930 points (2nd)
EVENT FIVE: Long jump
Johnson-Thompson: 6.68m, 1066 points (1st)
Thiam: 6.60m, 1040 points (2nd)
EVENT SIX: Javelin
Thiam: 57.91m, 1014 points (1st)
Johnson-Thompson: 42.16m, 709 points (2nd)
EVENT SEVEN: 800m
Thiam: 2:19.35, final score: 6816 (1st)
Johnson-Thompson: 2:09.84, final score: 6759 (1st)
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