The 31-year-old was moving up on the inside of race winner Chris Froome (Sky) when he got boxed in and almost crashed into his former teammate and the barrier with about 500m to go.
Dan Martin (Etixx-QuickStep) attacked from the outside at the same time to move into third overall behind Romain Bardet (AG2R).
“I was there but then, I don’t know what happened, the next thing I was nearly in the barriers and had to stop,” Porte said. “That’s when the group went and that’s where my podium was lost.
“To almost crash in the last 500m or so it’s a disappointing way to end a fantastic week. To be honest, I thought I had third.”
Porte was visibly frustrated as he crossed the finish line in Superdevoluy but speaking later by the team bus didn’t blame Froome for what he described as a race incident.
“His team put him almost into the barriers,” Porte said. “He was telling them to go left and for some reason they went right. It’s just a racing incident. I’m sure nobody meant to do it, it’s just everybody is on their limit and that’s just one of those things that happens.
“But I think it will keep me hungry for July.”
Froome in a winner’s press conference was sympathetic to Porte, who he rates a genuine threat ahead of the Tour de France based on the Australian’s overall performance.
“I feel really bad for Richie Porte because he deserves second place in this race. I think both Richie and I took a gap in the final because we got stuck against the barriers,” Froome said.
Porte will now embark on a team altitude training camp in final preparation for his career first Tour de France title attempt alongside BMC co-captain Tejay van Garderen.
“I’m quite happy with the form and the way things are lining up for July,” he said. “I think I can sharpen up for a hard July.”