Birmingham gymnast Thomas, 22, produced a highlight on the vault with a score of 16.025.
But he fell from the parallel bars and high bar to end his hopes of reaching the podium, scoring 85.700 in total.
Keatings is expected to return to action in next week’s Glasgow World Cup.
In Friday evening’s women’s all-around final, Whelan suffered an early mishap as she fell at the start of her uneven bars routine.
After that, both Whelan (total score: 54.175) and Francis (53.375) delivered clean routines but both are let down by comparatively low difficulty scores.
Only with greater difficulty can they threaten the highest echelons of the women’s sport, Dementyeva posting a winning overall score of 57.475.
With more difficulty comes more risk, and Russian superstar Mustafina collapsed following a painful landing in which her left knee was seen to wobble awkwardly.
The fall ruined her attempt at gold in all five women’s events at this tournament – and potentially sets her back for this year’s World Championships in October.
She joins Britain’s Theo Seager on the sidelines but Mustafina will hope her injury is not as serious.
British Gymnastics have yet to confirm the extent of Seager’s injury, sustained in training on Thursday, but BBC Sport understands he could be facing a lay-off until the end of the year with ligament damage.
Back on the mat, Britain will look for more success on Saturday and Sunday as the individual apparatus finals begin – four for the women and six for the men.
On Saturday, Purvis and Thomas take part in the floor final, Smith goes for pommel gold and Beth Tweddle defends her European uneven bars title.