ARTETA named a side with six players aged 20 or under and they looked in control, especially in the second half, as they beat a team which had not lost in 19 home games and had won their previous 10.
Pompey played well in the first half but trailed to Sokratis Papastathopoulos’ volley from Reiss Nelson’s cross just before the break.
Eddie Nketiah bundled home from close range from another Nelson cross to wrap up the victory six minutes after the restart.
Pompey’s only shot on target came in the second half, with substitute Ronan Curtis’ effort saved.
“I’m really pleased with them [the youngsters],” Arteta told BBC Sport. “I’m enjoying working with the players. They deserve a chance. It’s always a risk but they’re worth the risk.
“It was a great atmosphere and Portsmouth made it difficult. We knew we’d have moments we could suffer but we reacted and got control of the game. We got two goals and could have had a few more.”
The other fifth-round ties are on Tuesday, Wednesday and Thursday. The quarter-final draw is on Wednesday at 11:50 Harare time (CAT) after Sheffield Wednesday v Manchester City.
Arsenal came into this game on the back of their shock Europa League exit to Olympiakos on Thursday.
Arteta – slightly surprisingly – made nine changes, with several fringe players starting, and defender Pablo Mari making his debut, despite the FA Cup being the only hope of silverware for the record 13-time winners.
They lost Lucas Torreira to injury in the first half, the midfielder was taken off on a stretcher after a tough but fair sliding tackle by James Bolton.
That was their only negative from the game at Fratton Park, though.
Left-back Bukayo Saka – one of the two players to keep their place from Thursday’s defeat – forced a save and Gabriel Martinelli, also 18, headed over the bar.
Sokratis opened the scoring with a wonderful volley from Nelson’s right-wing cross.
And Nketiah scored his third goal since his loan spell at Leeds was cut short when he controlled Nelson’s cross before rifling into the roof of the net from close range.
From that point on Arsenal looked comfortable. They extended their unbeaten run against Portsmouth to 22 games and have not lost to them since 1958.
“There is a long way to go [in the FA Cup],” said Arteta. “But we’re on the right path. We’ll see what happens in the draw. We’ll keep going because we love this competition.”
This was something of a bonus match for Portsmouth, who are third in League One and pushing for promotion.
That was reflected by their starting line-up with their two top scorers – Curtis and John Marquis – and captain Tom Naylor on the bench.
Kenny Jackett’s side played well in the first half, with eight shots – but Curtis’ 73rd-minute effort from the corner of the box was their only one on target.
Arguably this was not even their biggest game of the week – they go to seventh-placed Peterborough on Saturday, with the clubs separated by only three points.
They also have a Wembley trip to come, against Salford City in the EFL Trophy final on 5 April.
“In terms of winning the game, getting the first goal would have been key and with the pressure we had, we needed one,” said Jackett.
“But after their second they dominated and it would have been a goal out of nothing from us. Then realistically we were playing damage limitation. My players didn’t buckle, kept going and that was good.”