The visitors thoroughly deserved to be ahead but Gylfi Sigurdsson drew Reading level with a superb free-kick in first-half stoppage time and held out for a point.
Sousa said: "In this game I am not happy with a point away from home. Bad decisions cost us the game. I consider it to be two points dropped."
Sousa was unhappy with the timekeeping that had allowed Reading to score during injury time in the first half.
"They signalled one minute of additional time but there was two minutes and forty seconds," he said.
"Once more we saw bad decisions against us but it is not something I want to talk about today.
"Officials are an important part of the game and they need to help. They need to be at the same level as the teams.
"It was a difficult game against a squad trying to impress a new manager. We played with great effort and personality."
The opening goal came nine minutes before the interval when Reading's defence was opened up by Angel Rangel's pass.
Pratley moved on to the ball from the left to shoot past Adam Federici's despairing dive. It was Pratley's fifth goal of the season and his third in the past two games.
Reading's equaliser came after Nathan Dyer fouled Sigurdsson.
The young Icelander took the resulting free-kick himself, curling the ball beyond Dorus de Vries into the top corner of the Swansea net for his sixth goal of the season
Reading's caretaker manager Brian McDermott has now seen his side come from behind to draw both of his games in charge - but he too was not happy with the draw.
"Swansea are a good side and give you all sorts of problems," he said.
"But you can't congratulate yourself when you only get one point at home.
"I had a text from Steve Coppell which said 'wng'. It took me a while to work it out, but then I realised it meant 'win next game'.
"That's been our motto for a while now at the Madejski and you can't do worse than follow the guidance of Steve, who has been the most successful manager Reading have had."
Asked if he might be considered a cheap option as manager McDermott replied.
"I am not that cheap," he added.
"I do want to be given the job here but that's a board decision. I am quite relaxed about it. I just do my work from day to day."