The race was part of her build-up to the European Cross Country Championships in Tilburg on 11 December where she will defend her title.
Yelling, 31, admitted her performance in Bilbao was "a bit of a disaster".
But she added: I'm not unduly bothered. I ran in France two weeks before the 2004 championships and had a shocker."
Yelling was given permission by the Great Britain selectors to miss Saturday's European trials in Liverpool to contest the higher-quality 5.6km race.
But she was some way off the pace of Hungarian winner Aniko Kalovics. Yelling now has a fortnight to fine-tune preparations for the defence of her European crown in Tilburg on 11 December.
Liz Yelling, Hayley's sister, led from the start as she won the women's European trial race at the UK Cross-Country Challenge in Liverpool to qualify for next month's championships in the Netherlands. She won the 6.5km event in a time of 22 minutes, 16 seconds.
Favourite Kate Reed retired in the last kilometre, and Natalie Harvey dropped back to fifth while Lisa Dobriskey was second and Lucy Elliott came third to also qualify.
Mo Farah won the men's 10km race for the second successive year to also book his place on the Great Britain team.
The full Great Britain team for the European Cross Country Championships:
Men: Mohamed Farah (Newham and Essex Beagles), Tom Humphries (Cannock and Stafford AC), Peter Riley (Leigh Harriers), Michael Skinner (Blackheath and Bromley), Frank Tickner (Wells City Harriers), Steve Vernon (Stockport Harriers).
Women: Eleanor Baker (South London Harriers), Lucy Elliott (Winchester and District AC), Natalie Harvey (South London Harriers), Kate Reed (Bristol AC), Hayley Yelling (Windsor, Slough, Eton and Hounslow AC), Liz Yelling (Bedford and County AC).
Junior Men: Keith Gerrard (Manx Harriers), Kelvin Hardy (Ipswich Harriers), Adam Hickey (Southend on Sea AC), Anthony Moran (Trafford AC), Tom Minshull (Trafford AC), Andy Vernon (Aldershot, Farnham and District AC).
Junior Women: Sian Edwards (Kettering Town Harriers), Morag MacLarty (Central AAC), Emily Pidgeon (Gloucester AC), Nicola Sykes (Bedford and County AC), Gemma Turtle (Shaftesbury Barnet Harriers), Stephanie Twell (Aldershot, Farnham and District AC).
MMIX
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It was so muddy, it kept sucking my heels out of my shoes