The 61-year-old claims that his team lost their "individual battles" and has says that the players will not be allowed to dwell on their Euro 2016 triumph in France.
"We started the game well, we dominated the first 15, 20 minutes but then we were dazzled by Switzerland and were a bit pragmatic," Santos told RTP.
"We conceded the only time that Switzerland were near our goal and afterwards we stepped back and allowed them to win individual battles – the European Championship has to be forgotten. We were not as strong as we usually are. We are in qualifying and that cannot happen."
Next up for Portugal is a home match against Andorra on October 7.