The Sun reported on Saturday morning that the duo were no longer training with the first-team squad after expressing their desire to leave Stamford Bridge in January.
Villas-Boas, speaking after Chelsea's 3-0 victory over Newcastle, has now confirmed that the pair are available for transfer and are not currently in his first-team plans.
"The conversation was fair and very, very frontal and direct with the players," he said. "The players have shown their interest in leaving the club - they have put in transfer requests for quite some time.
"They are top, top professionals - their professionalism and integrity is never in question - but at this moment and with the recent from and results, we have decided just to try to get the group together, and we have decided to assign different training times for Anelka and Alex.
"Again, it was a frontal and direct conversation. The players were fantastic in assuming it. The group was informed and they took on board the decision.
"The transfer request was accepted - it doesn't mean that it will happen, and if it doesn't happen, the players will return to full training."
Alex and Anelka both featured in Tuesday's 2-0 Carling Cup defeat to Liverpool but were not included in the squad for the trip to Newcastle.