The Swans went 1-0 up against the run of play in the 43rd minute at the Reebok Stadium through Luke Moore's deft chip, but Pratley, who left the Welsh side to join the Trotters in the summer, squared things by heading home an equaliser in first half stoppage time before Chris Eagles settled the fourth-round tie 11 minutes after the break.
Pratley has struggled to make much of an impact since his transfer to Bolton but might have scored three times today, following up his goal - which he celebrated in a restrained manner - with an effort that hit the crossbar and another that went narrowly wide, and manager Coyle was keen to praise the 26-year-old's all-round performance.
"I think Darren has probably been a bit frustrated at times this year," Coyle said.
"He is known as an attacking midfielder and he has had chances in various games, hitting the woodwork and seeing goalkeepers make good saves.
"It was great to see him hit the back of the net today and he could have had a hat-trick.
"We made three changes and Darren was one of them, and it was great to see the energy that he brought to the team.
"When he scored his goal he was very respectful of his former club and the fans with his reaction.
"He didn't over-celebrate, although he would have been well placed to have done so I think given that they were chanting at him.
"It was certainly a great answer from the lad and he showed his class with the celebration."
Swansea boss Brendan Rodgers - Pratley's manager last season - admitted he was also happy for the player, even if he was unsure whether or not the goal should have stood.
"It was a decent header, although I felt he was probably just a fraction offside when the ball came in," Rodgers said.
"But we should never have got to that point.
"I am pleased for Darren because he is a good lad, he has decided to leave Swansea and move here and maybe it hasn't quite worked out how he wanted.
"There is no doubt that he will show he is a really good player for Bolton."
The Trotters' winner came when Swansea goalkeeper Gerhard Tremmel - who replaced Michel Vorm in one of 10 adjustments to the visitors' first XI - parried Martin Petrov's shot, allowing Eagles to tuck the ball into the corner.
Rodgers refused to single Tremmel out for criticism, but felt mistakes on his team's part had ultimately proved to be their undoing.
"There is no blame attached to him," Rodgers said.
"I feel I have the number one goalkeeper in the league in Michel Vorm and Gerhard offers a wonderful support to him.
"He doesn't get a lot of game time and he is a good guy. There is certainly no blame attached, but we could have prevented their move for the second goal."
