Strikes from teenager Jack Barthram and Peterborough loanee Nicky Ajose cancelled out Andre Blackman's early effort but the off-form Pilgrims could be proud of their performance against the League One promotion candidates.
Owers said: "I felt we worked very hard but we probably struggled to come to terms with their system with them playing 3-5-2 and having an overload in the middle of the park.
"Having said that we stuck to our guns, I thought we came to terms with it and matched up to them second half and we probably finished the stronger of the two teams.
"Andre did really well to get the early goal, he got in down the left-hand side and I thought it would settle everyone down.
"But Swindon are a good team with some really good players and they have players with Premier League quality."