Marsaxlokk and Ħamrun Spartans had no margin for error to secure the second spot, and in the end, it was the Southerners who prevailed with a routine 3-2 victory over Naxxar Lions.
On the other hand, the Spartans, despite producing an improved performance than in recent weeks and creating better chances, still came unstuck against a clinical Valletta side who took the chances that came their way and prevailed 2-1.
The win also ensured that Valletta will force their way into the title battle as they will join Floriana, Marsaxlokk and Ħamrun Spartans in the Final Four.
The Citizens will be up against their fierce rivals, Floriana, in the Top Four semi-final, while Ħamrun Spartans will take on Marsaxlokk, with both matches to be played on May 9.
In the top match of the day between Valletta and Ħamrun, Spartans coach Giacomo Modica made four changes to his starting formation as Emerson Marcelina was back at the heart of defence at the expense of Ognjen Bjelicic.
Jonny, Damir Ceter, and Kleri Serber were also handed a starting berth at the expense of Sven Xerri, Blessing Ekele, and Eder.
Ħamrun Spartans started brightly, and they came close after four minutes when Matthew Guillaumier found Matias Garcia, who hit a thumping drive that was brilliantly pushed away by Maringa.
Valletta tried to hit back, but it was Ħamrun who threatened again on 17 minutes when Jonny sped forward and found Kleri Serber on the edge of the area, and his curling drive was pushed away by Maringa.
The Valletta goalkeeper continued to frustrate the Spartans as five minutes later, he was well placed to push away Ceter’s firm shot.
Ħamrun’s best chance arrived on 32 minutes when Serber played in Mbong, whose low cross was met by Ceter but his effort came off the upright with Maringa beaten.
A minute later, Serber was again close but his drive flew just past the upright.
Just before the break, the Spartans suffered a blow as Ryan Camenzuli suffered an injury following a challenge by Diogo Tavares. Sven Xerri was brought on in his place at the start of the second half.
Valletta also made two changes at the break as Thiago Aldama and Jackson Mendoza replaced Steijn Meijer
Ħamrun thought they scored on 49 minutes. Jonny sent a low cross inside the area and Ceter was blocked from a few metres out, but in came Guillaumier who tumbled the ball home.
But the goal was annulled as Jonny was in an offside position.
Instead, it was Valletta who struck on 53 minutes when Mendoza hit a thumping drive from the edge of the area with the ball flying into the top corner of the net.
But Ħamrun hit back strongly, and they levelled matters three minutes later when Jonny played in Ceter, who was blocked by the onrushing Maringa, but Compri was on hand to fire home.
The goal lifted the Spartans, and they almost grabbed a second 11 minutes from time when Danilo Bulevardi played in Mbong, but his shot was pushed away by Maringa.
At the other end, Bonello came to Ħamrun’s rescue when he denied Tavares, and the ball fell Paiber whose shot was blocked to a corner.
But from the ensuing corner, substitute Adebayo headed home to put Valletta back in front.
There could have been more misery for the Spartans as on 86 minutes, Bulevardi was shown a straight red card for kicking his opponent. But after a Football Video Support review, the referee overturned his decision and booked the Italian midfielder.
Marsaxlokk thought they were off to a fine start as they had the ball into the Naxxar net after only eight minutes of play.
Domantas Simkus received the ball on the edge of the area, and his thumping drive flew into the net.
However, referee Philip Farrugia annulled the goal after consulting the Football Video Support for a foul by Linden on a Naxxar defender.
At the Tony Bezzina, Stadium, Marsaxlokk took the lead on 28 minutes when Dodo Soares sent a low pass across the area, and James Kirby was on hand to stab home.
Naxxar Lions managed to draw level a minute from the break when Vitinho took full advantage of some hesitation in the Marsaxlokk defence and the Brazilian managed to fire the ball past goalkeeper Christoffer Mafoumbi, despite being in a close angle.
But that setback failed to derail Marsaxlokk as a minute later they restored their lead.
Ulises Arias hit a thumping drive that was partially blocked by Mathias Debono but in came Kirby who fired into an empty net.
Marsaxlokk remained in control and they managed to seal the points with a third goal on 73 minutes.
From a lateral free-kick, Niki hit a curling drive that flew into the net.
Naxxar did manage to pull a goal back late on through Gabriel Goncalves.
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