Slovakian Hamsik came on as a late substitute against Parma on Saturday but was forced off just nine minutes later after suffering the knock.
Rafael Benitez's men will be looking to regroup ahead of a trip to Dortmund where a draw will be enough to send them into the knock-out stages ahead of their final Group F game at home to Arsenal on December 11.
Napoli currently sit second on the same points as Arsenal, who have a superior goals difference, but have a three-point cushion on Dortmund, who face Marseille away in their final group game.
Marseille missing Payet
Marseille forward Dimitri Payet will miss Tuesday's trip to Arsenal due to a swollen knee, the French team said Sunday. The 26-year-old, who scored in Friday night's 3-1 win at Ajaccio, did not take part in training on Sunday.
"Given the commitments of the coming weeks, the staff have decided not to take any risks," said the Marseille statement. The south coast club have already been eliminated from the Champions League having lost all four matches so far, while Arsenal lead Napoli at the top of group F after three wins.
Xavi returns, Adriano out
Meanwhile, injury-ravaged Barcelona will be bolstered by the return of Xavi Hernandez for their Champions League visit to Ajax on Tuesday, but will be without full-back Adriano.
The Brazilian suffered a twisted ankle in Saturday's 4-0 win over Granada that saw the Catalans maintain their three-point lead at the top of La Liga. Xavi missed that game due to a hamstring strain but took part in training on Sunday and will travel with the squad to Amsterdam.
Coach Gerardo Martino is still without the services of Lionel Messi, Victor Valdes, Jordi Alba and Dani Alves. However, the four-time European champions have already sealed their place in the last-16 of this year's competition and need just a point from their remaining two games to guarantee finishing top of Group H.
Leverkusen's Sam out of Man Utd clash
Germany winger Sidney Sam has been ruled out of Bayer Leverkusen's clash at home to Manchester United on Wednesday after tearing a thigh muscle.
The 25-year-old limped off after just four minutes of Leverkusen's 1-0 Bundesliga win at Hertha Berlin on Saturday and a scan on Sunday revealed the extent of the injury.
"The loss of Sidney is very bad news," Bayer's director of sport Rudi Voeller said on the club's website. "This is the game of games for us in the Champions League, we have to put all our power and effort into it, just without Sidney."
Leverkusen have not said how long Sam is expected to be out for, but with less than a month left before the winter break, the Germany winger faces a race against time to be fit again in 2013. Leverkusen are second in Group A, just one point behind David Moyes's English Premier League side.