Ultimately, it was Quick-Step Floors' Alaphilippe who crossed the line in front in a time of 4.26.58 with UAE Team Emirates' Martin and Sky's Thomas in hot pursuit.
Geraint Thomas (Team Sky) looked to have done enough to move into the overall lead as his teammate and previous race leader, Michal Kwiatkowski, dropped away in the final kilometre, but it was another Team Sky rider who took over yellow jersey duties.
Alaphilippe wins Criterium Stage 4, Moscon claims lead
In the classification, the Italian is now six seconds ahead of both Kwiatkowski and Thomas.
"I think these four days are the hardest four days I've raced in a one-week stage race", said Thomas. The Dauphine is the main warm-up race for the July 7-29 Tour de France.More news: Trump eyes pardon for late boxing hero Muhammad Ali
So, I chose to work as hard as possible for a stage victory. "I'll enjoy tomorrow, or I'll try to enjoy it in the jersey and defend it but it's super hard". I had good legs in training all year, but it hasn't come together in races for some reason.
"It's great in the new team environment".More news: White House adviser says Canada's Justin Trudeau 'stabbed us in the back'
In the final steep climb Martin, trailing the overall leaders by nearly three minutes, was allowed to escape as the overall contenders eyed each-other.
Saturday's stage is nearly the same as the Tour de France stage 16 with four major climbs on the menu and a summit finish at la Rosiere.More news: Trump's top economic adviser accuses Trudeau of back-stabbing after G7 summit
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