The world record holder clocked 30.58 seconds for the one-length race to beat Great Britain’s Sophie Taylor, who clocked 30.77.
Despite being the fastest time this year, it is well off her own world record, which stands at 29.48.
There was disappointment for Meilutyte’s Leander team-mate Antony James, who just missed out on a medal in the men’s 100m butterfly event on the final day of the championships in London.
Former Commonwealth Games silver medallist James, who competed at the 2012 Olympics, finished fourth in a time of 52.88 seconds. Loughborough’s Tom Laxton won the title in 52.40, with Braxston Timm second in 52.72 and Adam Barrett third in 52.74.
Leander Shauna Lee reached the final of the women’s 200m freestyle event, where she finished seventh in 2:00.64.
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