The West Midlands outfit were able to come through by a 4-0 scoreline on Thursday night as they comfortably booked a spot in the Europa Conference League quarter-finals.
Watkins opened the scoring at Villa Park before Leon Bailey, Jhon Duran and Moussa Diaby all netted in the second half as their Dutch opponents offered minimal threat.
However, Watkins needed to be withdrawn during the opening 45 minutes, a consequence of suffering a knee issue when challenging Ajax goalkeeper Diant Ramaj.
Having mistimed the tackle, Watkins was booked after receiving several minutes of treatment, but he eventually got to his feet and put Villa ahead with a brilliantly-taken header.
Soon afterwards, though, Watkins signalled to the bench that he needed to come off, the England international being partially helped off the pitch before hobbling down the tunnel.
With West Ham United to come on Sunday and Watkins having been selected for the Three Lions' upcoming matches with Brazil and Belgium, there were naturally concerns that he would be at least absent for those fixtures and many more ahead.
Nevertheless, Emery has stated the opposite, telling TNT Sports that Watkins has suffered a cut, rather than a muscle or ligament injury.
He said: "It's no more than a cut on the knee. Maybe he could be available for Sunday [against West Ham] but we'll have to wait and see."
Bailey told the same broadcaster that Watkins - who was seemingly taken precautions - had suffered "an open wound".
Watkins has now scored 21 goals in all competitions this season, while understudy Duran netted his third in what was an impressive display from the substitutes' bench on his own return a spell on the sidelines.