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It was Hajduk, not the Red Star, who would eventually have the last laugh in the Cup. On May 8, 1991, the same rivals met at the same venue, the JNA Stadium in Belgrade, in the last final played before Yugoslavia fell apart. The tense political standoff of the day was mirrored in a strange atmosphere on the stands. The Whites won the game thanks to an excellent goal by Alen Bokšić, and hugely disappointed the Red Star'a fans, after they were crowned as European champions only days before.
A month after the final, Hajduk played their very last game in the Yugoslav championship, beating Proleter of Zrenjanin 3-2 away. The last goal came from Ardijan Kozniku, whose prolific scoring would make a mark on the first years of the Croatian football league.
UEFA disallowed Hajduk to host Tottenham in Split in the first round of the Cup Winners' Cup. The game was thus played in the Austrian town of Linz, where Mario Novaković scored for a 1-0 victory. The English team won the second leg at their White Hart Lane stadium 2-0, eliminating the Whites from European competition for the third time.
The inaugural Croatian championship kicked off in February 1992. Hajduk's unstoppable sequence was opened by a 3-1 win over Istra. The league came to a close on June 13, when Hajduk overcame Šibenik 4-1 to become the first ever champions of Croatia. Moreover, Kozniku, having scored 12, was the league's top goalscorer.
Hajduk did not manage to defend the title the following season, but did win the Croatian Cup for the first time, in a two-leg final against Croatia of Zagreb (4-1, 1-2).
The 1993/94 season saw the debut of coach Ivan Katalinić's excellent team, set back early on by the departures of Novaković and Jeličić, who joined the archrivals from Zagreb. The war once again prevented Hajduk from playing the opening round of the Cup Winners' Cup in Split. The mighty Ajax of Amsterdam was thus hosted in Ljubljana. In an unforgettable atmosphere on the Bežigrad Stadium, Ivica Mornar scored for a 1-0 victory. The return leg proved to be the greatest single defeat for Hajduk in European cups with a six-zero scoreline. Even so, the result was not really a disaster, as the opponents were perhaps one of Europe's greatest-ever teams (featuring such names as Van der Sar, the de Boer brothers, Davids, Seedorf, Rijkaard, Kluivert, Kanu, Litmanen…) and in fact the Ljubljana game was their only defeat in Europe in either that season or the next.
The season did not end in disappointment, as the domestic league was won in a crunch tie against Zagreb on their stadium in Kranjčevićeva street, the deciding goal coming with a free kick by Zoran Vulić.
The following season was a time of great triumph for the Whites. Domestically, the club's only Croatian Double crown came after Croatia of Zagreb was beaten both in the league and also in the Cup final (3-2, 1-0). These achievements were matched by European success. Two victories over Polish champions Legia (1-0, 4-0) saw Hajduk qualified for the Champions League, in the debut season of that most prestigious club competition. The Whites staged an upset by progressing from the group stage after victories over Anderlecht of Belgium and Steaua of Romania. However, the quarter final draw again paired Hajduk with Ajax, the hardest possible adversary, who would go on to win the European title. The first leg at Poljud ended in a promising scoreless draw, but the second leg at Amsterdam finished 0-3 in favor of the hosts.
In the summer of 1995, Hajduk attempted another Champions League qualification. The opponents were Panathinaikos of Athens, where the first leg was played at an empty stadium, this being a fine for the Greek fans' previous misbehavior. The 0-0 result was considered promising, but the return leg once again could not be played in Split. The Greeks were therefore hosted in Rijeka, where Hajduk was greatly unfortunate in only managing a 1-1 draw. This meant not only elimination from further competition, but also a severe financial setback.
In the second half of the 1990s, the club did not manage to recover from this, and domestically mostly played second fiddle to Croatia Zagreb. One silver lining was the third Croatian Cup, which arrived at Poljud in 2000. The team coached by Petar Nadoveza, featuring such youth academy prodigies as Pletikosa, Miladin and Leko, overcame the Zagreb archrivals (again renamed Dinamo) in a two-leg final by a scoreline of 2-0 and 0-1.
Material from publications by Jurica Gizdić used with permission: Hajduk in Official Competitions, 100 Years of Hajduk, Hajduk's Presidents and Hajduk's Coaches. The History of Hajduk by decades was prepared by Dag Baldasar.