Brazil international Neymar had been in contention to feature in Sunday's Primera Division opener against Elche, after recovering from the fractured veterbra that he sustained during this summer's World Cup, but he picked up an ankle knock on the eve of the game at Camp Nou.
Belgium defender Vermaelen had yet to fully recover from the hamstring strain that troubled him at Brazil 2014, while Germany goalkeeper Ter Stegen took a blow to his back during training earlier in August.
All three players featured in Tuesday's session however, although they worked separately from the rest of the group.
Barcelona kicked off their Primera Division campaign with an impressive 3-0 win over Elche in what was Luis Enrique's first competitive outing as coach.
Next up for the Catalans is a trip to El Madrigal on Sunday to take on Villarreal.