Rasheed Muhammad, 43, and Ramzan Rizwan, 25, were charged at the state court for killing 59-year-old Muhammad Noor.
If found guilty, the duo could get death penalty.
The accused have been remanded for further investigations and their case would be heard on June 20, The Straits Times reported.
Noor's legless body was found in a suitcase on Wednesday night on the Syed Alwi Road in Little India, a precinct of Indian-origin businesses, budget class hotels, eateries and pubs popular among South Asians.
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The suspects were arrested on Thursday.
All three were reportedly from the same Pakistani village and had come to Singapore last month to sell tissue paper.
They were staying at a Rowell Road lodging house during their time here, the report said.