Villa had a stellar start in the revamped Champions League with goals from Youri Tielemans, Jacob Ramsey, and Amadou Onana securing a well-earned win for Emery's team in Bern.
Watkins, meanwhile, found the net with a thumping finish in the first half but the goal was ruled out after the ball struck his arm moments before his strike.
The 28-year-old also took a knock in the first half and was then replaced by Jhon Duran, who also had a goal ruled hour, on the hour mark.
Watkins was seen sitting on the bench with ice strapped to his right ankle, sparking concerns over his fitness ahead of Villa’s Premier League clash against Wolves on Saturday.
When asked about Watkins’ injury after Villa’s win, Emery said: ‘Yes, he’s okay.
‘Now we have as well Jhon Duran in good form. They can play together.
‘But something as well, today he plays 60 minutes, another 30 minutes for Duran. Of course, we need both, together, individually, adding his capacity on the pitch in the time we need.’
Emery also believes playing in the Champions League will play a major role in helping his squad develop.
‘The most important thing is the process we are doing here,’ Emery said.
‘Some players don’t have experiences at the level of the Champions League and others, yes.
‘We have to build and create a new way. The way we created last year in the Conference League was fantastic, even if we did not get to the final.
‘We are using the experiences we are adding to do our best playing in the Champions League, starting with the respect we have for every team and with playing away always being very difficult.
‘Of course, Our supporters are following us here and helping us. We have to be strong and be together even when we are playing away from Villa Park.’
Villa’s next game in the Champions League is at home to Bayern Munich on October 2.
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