Belgian Philipsen sprints to Tour de France third stage win
The Alpecin rider appeared to cut off a rival as he moved to his right in the finale, but the race commissioners approved the Belgian's win, ahead of Phil Bauhaus and Caleb Ewan.
"It was tense but it's the Tour de France," said Philipsen at the finish.
"Everyone wanted to put everything into this sprint."
English rider Adam Yates of the UAE Team retained the overall lead as all the chief contenders finished together after a 182km run from northern Spain to Bayonne.
Sunday's star Victor Lafay, who remained fourth overall, retained the sprint points green jersey, while 2020 and 2021 champion Tadej Pogacar kept second place and the best young rider's white tunic.
Philipsen attracted ridicule at the Tour de France last year for celebrating what he believed to be a stage win when in fact Wout van Aert had already crossed the line on a solo escape.
A Netflix series about the 2022 Tour then nicknamed him 'Jasper the disaster'.
Orange hats and green and red Basque flags were an ever present on the early climbs as American rider Neilson Powless extended his lead in the mountain classification.
As the Tour caravan crossed the border fans cheered breakaway rider Frenchman Laurent Pichon of Arkea Samsic with every push of the pedals but he was caught 30km from home.
Tuesday's stage four is a largely flat 182km run from Dax to Nogaro with a racing circuit finish line which should culminate in another mass sprint.