The Gunners were left frustrated by their guests at the Emirates in the first half, with a steely Southampton showing a marketable improvement from their dismal 3-1 defeat at Bournemouth last time out.
A host of changes saw Jorginho, Gabriel Jesus and Raheem Sterling brought into the starting lineup, the latter making his first Premier League start for the club.
But the hosts were shellshocked when Cameron Archer broke away and curled an effort past David Raya in the 55th minute to open the scoring, only for Havertz to hit back immediately after Saka capitalised on a defensive error.
Saka then laid a perfect cross for substitute Martinelli to tap home at the back post and then with minutes remaining, fired past his former Arsenal team-mate Aaron Ramsdale with a clinical finish on his weaker foot.
Here, Express Sport takes a look at how the Arsenal players fared against their Southampton counterparts...
There was little that Raya could do to prevent Archer's goal and the Spanish stopper had little to do outside of picking the ball out of his net. He was nearly left red-faced by Taylor Hardwood-Bellis at a late corner when Raya failed to punch clear, only for the resulting header to crash back off the bar.
Defence
Thomas Partey - 5
Returning to the right-back role he manned at the beginning of last season, Thomas Partey struggled to have much of an impact on the match. He failed to provide an overlap option when Saka was up against two markers, but neither moved into midfield to help overload with Jorginho and Declan Rice.
He was caught between positions and allowed space in the channel to open up for Archer, with Partey unable to close down Mateus Fernandes in time either to release the goalscorer. When attempting to keep Southampton at bay, while leading 2-1 in the final few moments of the game, Partey was withdrawn for the return of Takehiro Tomiyasu.
William Saliba - 6
William Saliba will feel that he could have done more to close down Archer, with the former Aston Villa striker given too much room to allow an effort to be curled around Raya.
Gabriel - 6
A quiet evening for Gabriel, who was not at fault for Archer's goal and this time could not get on the end of a Saka set-piece to impact the game at the other end of the pitch.
Calafiori is quickly turning into an Emirates fan favourite and it is no surprise with performances such as this one against Southampton.
The Italian was under pressure early into the contest when a long ball dropped over his head and he was surrounded by Ross Stewart and Tyler Dibling. But the left-back calmly brought the ball down and then jinked past another visiting player, escaping danger with relative ease.
William Saliba and Riccardo Calafiori in action against Southampton. (Image: Getty)
Midfield
Jorginho - 7
Jorginho brought a much-needed calm to the Arsenal midfield, illustrated early with a clip around the corner to Havertz, a pass neither Partey nor Rice would have made during their time together as a midfield duo.
He was brought off after the hour mark but his presence allowed Rice to crash into the box and move forward, rather than sit deep and help Partey build possession, a visibly more fluid balance that Mikel Arteta will surely consider going forward. Especially against teams that Arsenal will dominate the ball against throughout.
Declan Rice - 6
It was a quiet afternoon for the former West Ham skipper but he put in a number of promising corners that Southampton just about dealt with. He did look more willing to move forward, thanks to the inclusion of Jorginho, but could not make a decisive contribution in the final third.
Given more of a free role, Havertz played off Jesus and flourished outside of his traditional number nine position, highlighted with a stunning finish to equalise moments after Southampton's opener.
He had plenty to do when released by Saka, tipping the ball around the scrambling defender and hitting his strike with enough power to leave Ramsdale without a hope of stopping the German from wheeling away in celebration.
He is now just the second Arsenal player to score in seven consecutive Emirates appearances, after Robin van Persie, with perhaps a few more similarities rising between the two as Havertz continues to make a mockery of his £65million fee.
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Essentially the matchwinner, having set up both goals, Saka was quieter than a week ago at home to Leicester but he was just as equally devastating in the final third.
He played the necessary ball for Havertz as their partnership continues to grow, before taking his time to pick out Martinelli at the back post to score the winner with an inch-perfect cross. Saka quietly delivered once again.
Then he put the game to bed with a clinical finish on his right foot, after the ball popped free in the area, he made no mistake to dispatch past Ramsdale and secure three points that had been in jeopardy once upon a time.
Gabriel Jesus - 5
Following the emergence of Havertz as a centre-forward, Jesus needs to take every opportunity to start in the Premier League with both hands.
However, he was unable to do so and was brought off after an hour with little impact on the match. He had a chance to send Saka in on goal in the first half, but opted against the pass, as Havertz provided more of an impact in attack while also moonlighting in midfield.
It was no surprise when he was taken off after 60 minutes for Leandro Trossard as Arsenal made a sharp improvement when the Belgian took his place.
Raheem Sterling - 5
On his first Premier League start for Arsenal, the Chelsea loanee made a bright start and appealed for a penalty after a collision inside the area, but the referee waved away Sterling's pleas.
He was unable to build on that quick beginning, however, and was dispossessed too easily for Archer's goal despite protests for a foul on the England man.
There were a few nearly-moments but Sterling, similarly to Jesus, flattered to deceive and Martinelli's goal will be bittersweet for the 29-year-old. His team got the three points thanks to it, but the Brazilian's place in the starting lineup ahead of Sterling was further cemented.
