In a bad second quarter for Capital, its breakfast show pulled in just 852,000 listeners, compared with 963,000 in the previous quarter and 1.08m a year ago.
It is a new low for the station and Vaughan, who inherited a 1.38m breakfast audience from Chris Tarrant in the spring of 2004.
Heart's Jamie Theakston could have overtaken Vaughan if he had held on to the 855,000 listeners he got last quarter, but he failed to do so.
With 820,000, he is in second place, narrowly ahead of Magic's Neil Fox, who got 803,000. Fox lost just 1,000 listeners from last quarter.
The next most-listened-to breakfast show was on Kiss, despite the station terminating veteran host Bam Bam's contract in April as a result of offensive on-air stunts and comments.
Temporary presenter Robin Banks will have enhanced his chances of a permanent deal by bringing in an extra 47,000 listeners to reach 705,000.
Virgin Radio's Christian O'Connell had a disappointing quarter, losing 42,000 listeners to hit 580,000. At his former station, Xfm, Lauren Laverne and Shaun Keaveny pulled in 327,000, down 13,000.
At LBC, rumoured Tory candidate for London Mayor Nick Ferrari shed 51,000 listeners at 351,000.
Nationally, Radio 1's Chris Moyes recovered convincingly, benefiting possibly from his appearance on 'Celebrity X-Factor', from losing listeners over the winter. He got 6.79m this quarter, more than 300,000 up from 6.32m in the first quarter.
On Radio 2, Terry Wogan performed similarly well, and is on 8.06m up from 7.77m.
However, Radio 4's 'The Today Programme' lost listeners, and is down from 6.12m to 5.87m.
Classic FM's Simon Bates was unchanged at 2.9m, but Virgin Radio's O'Connell lost almost as many national listeners as Johnny Vaughan did in London. Having brought in 1.25m last quarter, he was down to 1.14m.
TalkSport's Alan Brazil dropped 29,000 listeners over the quarter, leaving him with 947,000.
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