Habitam Alemu of Ethiopia completed only 100 seconds from the Scotsman.
The Muir one-minute 59.50-second stamp was 0.19 seconds quicker than its time in a year ago’s Scottish Indoor Championships.
The 25-year-old will contend in the 3,000-meter British title this end of the week.
The Birmingham occasion fills in as a test for the European indoor title, which will occur in Glasgow one month from now.
Muir won gold awards of more than 1,500 and 3,000 meters at Belgrade’s European Indoors in 2017.