Johnson-Thompson again flirted with the world record, eventually finishing with 4,983 points – just 30 short of Nataliya Dobrynska's mark from 2012 – ahead of team-mate Niamh Emerson.
The timetable in Glasgow was not kind to Muir’s hopes of repeating her double heroics from Belgrade two years ago, but she justified her status as favourite by shrugging off any tiredness to cruise to glory in Friday’s final event.
Muir waited until the bell to launch a devastating attack, leaving Germany’s Konstanze Klosterhalfen trailing in her wake to win in 8:30.61. GB’s Melissa Courtney took bronze.
Marvellous Muir wins 3000m gold in style
Johnson-Thompson's accession to top step on the podium seemed a formality before the competition had even started, following the news that Olympic and world champion Nafi Thiam would miss the event.
And the Liverpudlian duly delivered in the opening session, setting a season’s best in the 60m hurdles (8.27s), equalling the pentathlon high jump championship record (1.96m) and breaking her personal best in the shot (13.15m).
Such was her dominance after three events that talk turned towards a possible world record. That would prove a stretch too far, with a solid but unspectacular long jump (6.53m) leaving too much to do over 800m.
How KJT stormed to pentathlon gold at the European Indoor Championships