The Colombian had a strong start to his race, running solidly inside the top ten, but then a mistake in the pits and a loose wheel caused him to drop down in the order.
However, an early final stop allowed him to get back in contention, when all the leaders pitted for the final time under caution a few laps later than him.
"We pitted basically as early - I think this race track, by tradition, you pick up so much in tyres, and track position is so important, everybody was running together," said Montoya.
"We decided to come in when we could make the 'green-white-checkered'. We probably could have come in earlier than that.
"I know I needed a little bit of cautions. But I had four or five more laps on the race track before I stopped, and still made it. So we were pretty good."
Montoya jumped from 33rd place following his final stop up to fourth when everyone completed their final stops.
He then moved up to second, dropped back to fourth before the last caution, and on the final restart he saw Denny Hamlin pass him after he ran wide when Sam Hornish Jr and Kasey Kahne made contact with him while battling for position into Turn 1.
The 33-year-old said he probably lost any chance of winning on that restart when Hamlin got by, but putting his second place into context, he feels good about moving up to eighth in the Cup standings and closer to his goal of making the series play-off.
"I think the biggest thing was where [Hamlin] was going to be," said Montoya. "I thought I had a car fast enough to hold [him]. I got hit in the last restart, and he passed me. I don't know.
"Ifs and buts out, my goal is making the Chase. That's the bigger picture. If I make the Chase, they won't remember this guy won the race, this one didn't.
"[Kyle Busch] won three races this year. He's probably like 150 points out or something. You know what I mean? They won't be talking that he won three races. They'll be talking he [didn't make] the Chase."
The Earnhardt Ganassi driver believes he may have a shot at the title if he is able to make the Chase, given the performance they have been able to show in the last few races.
"What we say with [crew chief] Brian is let's get into the Chase and then let's have some fun," said Montoya. "I think we got fast race cars. I think we're just starting to push more the envelope with everything we do. I think if we make it, we might have a shot at this."
Next weekend Montoya hopes to make the most in the final road course event of the year at Watkins Glen, where he anticipates being more competitive than what he was back in June at Sonoma.
"For us going to a road course is good, especially that one. In Sonoma our car never runs good," he said. "Watkins Glen we normally got a really good car.
"For us, if we can get a top five out of there, I know we can probably win the race, but if we get a top five out of there, the points for the Chase would be huge."
Montoya's first top five finish of the season puts him 169 points ahead of 13th place in the driver standings with only five races left before the Chase for the Cup begins.
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