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 manager Coyle was keen to praise the 26-year-old's all-round performance. He said: "I think Darren has probably been a bit frustrated at times this year."
He added: "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 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."