The South Korean finished clinically, and his strike partner Harry Kane bagged a brace, as Tottenham won 3-0 to go within a point of their bitter rivals.
That took Son’s goal tally to 21, just one behind Mohamed Salah in the Premier League golden boot race.
The forward said during the week that he wasn’t thinking about winning the prestigious prize for top goal scorer.
However Son showed how desperate he was to take the golden boot off the Egyptian King in the 71st minute.
As the fourth official held up the number seven showing Son was to be replaced by Lucas Moura, the South Korean looked furious.
He was glowering and shaking his head as he walked off, and Pierre-Emile Hojbjerg had to console him as he was leaving the field.
Conte tried to give his star player a huge, but Son wasn’t having it at first.
He clearly wanted to stay on the pitch, and go past Mohamed Salah while Arsenal were down to 10 men.
At full time, Son was smiling again and his manager was giving a cuddle to make up.
When quizzed about it after the game, the Spurs ace denied he was chasing the golden boot.
He told Sky Sports’ Geoff Shreeves: “I want to play always, what can I say.
“It’s the gaffer’s decision, I need to accept.
“He said we have an important game on Sunday.
“I’m not angry, I’m just disappointed I came off - I really wanted to keep playing.
“It wasn’t the goals 100% though they were one man less, I just want to play.
“But we have an important game on Sunday.”
And Conte gave a wry chuckle when he was asked about his talisman’s reaction.
“I know for sure Sonny wanted to continue to play and to score,” he said.
“But I had to think not only this game, but later, he needs to rest and recover well.
“I wanted to make a substitution and give them a bit of rest.”
Spurs are playing Burnley at lunchtime on Sunday at home, while Arsenal face Newcastle at St James’ Park on Monday night.