After Stuart Armstrong gave the home side the lead early on, both were on target before the break as the Gunners turned the game around.
Moreover, Saka created a goal for Alexandre Lacazette in the second half to seal the points.
The 19-year-old has been in excellent form throughout the season and was praised by his coach in the aftermath.
“He’s been very consistent this season,” Arteta told BT Sport. “We’ve played him in many different positions and he’s been very versatile. He’s very good on the right, his link up play is good, his assisting play is really strong. It was another very good performance today.”
Meanwhile, Pepe has often been a target for criticism at Arsenal following a big-money move from Lille 18 months ago, but has a fan in the Spaniard.
“He was really good again. He scored a goal, was involved in many good actions, he worked very hard. He deserved his chance today and he took it,” the manager said.
Overall, Arteta was delighted with what he saw, particularly after his side lost 1-0 to Saints in the FA Cup at the weekend.
“We were really good right from the start,” he said. “We were really good on the ball. We improved our build up play, our pressing was excellent, when we had to defend deeper, we managed that well. Overall, it was a very good performance.
“It’s tough to win here. Teams really struggle against them. The way we played against them, the way we managed the game, the way we understood what the game required, we showed our intelligence as a team.
“We’ve still got a lot to do, a lot to recover. We have to be humble, prepare well and play the next game. We haven’t done anything.”
Victory put Arsenal eighth in the league.