Chris Eagles put the shine on a fine Trotters performance with an injury-time strike after first-half efforts from Nigel Reo-Coker and David Ngog sandwiched a superb Mohamed Diame strike.
Coyle was particularly pleased with the way his side recovered from conceding Diame's equaliser, plus the blow of a missed penalty from Kevin Davies when the game was still in the balance.
Coyle said: "The biggest thing today was having conceded the equaliser from a wonder strike it would have been easy for this group to feel sorry for themselves.
"Then in the second half with the missed penalty you start to wonder if it's going to be our day. But we knuckled down from start to finish and I thought we were magnificent."
Coyle is adamant the only way is up for his side, with a nightmare series of fixtures in the past and a growing confidence which was restored during the international break.
Coyle added: "Ordinarily during an international break you would give the players some days off but we had only four or five away and we came in every day.
"We'd played all the elite clubs together but when you lose games confidence is fragile. We had to try to address it and we got a real feel-good factor.
"The two weeks were great. We got them working hard and we got a smile back on their faces. I said I wanted them to transmit how they trained into the game today and they did that."
Wigan boss Roberto Martinez insists there is still enough quality in his squad but bemoaned more silly mistakes after his side's fifth league defeat in a row.
Martinez said: "I feel really disappointed because we gifted Bolton the three points. The hardest thing is to score goals and we made it very easy for them.
"Sometimes you get the wrong dynamic and that's where we are the moment. Apart from that I saw my team working very hard and if we had gone in level at half-time we could have won the game.
"Bolton came here in a physical derby with their physical aspects but they didn't have to show too much flair to score goals. That's disappointing and it's why we lost.
"It is now a matter of changing the wrong dynamics, keeping a clean sheet and sensing danger. It is not that we are not good enough, it is that we are very poor in our decisions."