Still, that second Test created another special moment.
"The best part was meeting the Queen," says Agar. "Michael Clarke introduced her to everyone and we had to address her as 'your majesty'.
"She came to me, shook my hand and said: 'This is your first time here, isn't it?' I said: 'It is.'
"She said: 'Good luck, have a good time.' I could not believe it. The Queen knew it was me."
Agar was "relieved" to be dropped after the second Test. The third, at Old Trafford, was the beginning of Lyon's 100 consecutive Tests. Agar, now 32, played three more Tests, none of them in the Ashes.
Hughes, Agar's batting partner on that day in Nottingham, was killed on the field little more than a year later, struck by a fatal blow to the neck batting in a Sheffield Shield match.
"I feel very lucky to have shared that with him," says Agar. "I had a photo of Phil up on my bedroom wall, playing one of his signature cut shots. Me and my brothers loved Phil.
"I was batting with someone I looked up to. Getting to share one of the biggest moments of my life so far, and learning about resilience, staying present and what that does in terms of performance is a huge lesson.
"He showed me that in real time. It was a special time we spent together. He was a beautiful man."
Two days after Hughes passed away in November 2014, Agar was playing in Perth for his club side University.
He was out for 98.
"It was spooky, actually," says Agar. "There was a big 408, his cap number, painted on the ground and there was a minute of silence. It was tough.
"I remember feeling quite focused. I was thinking about our innings, what he was telling me at that time. On 98 I nicked a ball to second slip. It was nice it happened that way."
98. The number for which Agar's Ashes career will forever be remembered.
"I've never thought about the two runs I didn't get," says Agar.
"The feeling for me has never changed. It has never been regret or disappointment.
"I'm just really happy for what happened that day."