Matthews has said repeatedly in the lead-up to the Tour that he is not where he would normally be physically, having prepared with the intention of helping Tom Dumoulin's push for the general classification.
He has nonetheless been a significant player in the early stages of the race and reinforced that with a stunning sprint to take second on the steep uphill finish in Epernay.
"I was not where I would have liked to have been today," said Matthews after the finish. "I was trying to convince myself that I wasn't tired but I was destroyed."
"I'm not happy with my shape. I really struggled today and it's only the third day. I didn't really enjoy that."
Alaphillipe attacked with just over 15 kilometres to race, shooting off towards the finish line and staying clear to take the stage and the yellow jersey. Matthews, for his part, exploded out of the chasing peloton in the final metres to overtake Jasper Stuyven (Trek-Segafredo).
"At the finish it was just everything I had left, and lucky it was good enough for second," Matthews said, who now sits 17 points behind Peter Sagan (BORA-hansgrohe) in the green jersey competition.
"I (rode with) pure heart...thinking about my baby, thinking about my wife. Although it was for second it was pretty beautiful in the end."
Matthews' poor shape impacted him heavily on the ascent of the Cote de Mutigny with the Australian in danger of losing contact with the peloton.
“On the categorised climb where Quickstep really pushed it and exploded the bunch I was almost dropped there,” said Matthews. “I had really good team mates around me who kept me motivated and brought me back to the front; to keep me in the race.
"It’s unfortunate that Alaphilippe stayed away because my sprint was really good and I really gave it everything I had to the finish. Today is a confidence booster for us going forwards.”
The next stage offers a chance for a flatter sprint, though with a few climbs in the final ten kilometres of the stage, sprinters who do make it through to the line will likely be a bit more fatigued than normal, perhaps giving Matthews an increased chance of his first stage win for the 2019 Tour.
