The 30-year-old hometown boxer started comfortably but lost his way in the middle of the 12-round contest with the Malawian, and the judges scored the main event 116-112 Chilemba, 116-115 Bellew and 114-114.
The winner was set to meet either champion Chad Dawson or first challenger Adonis Stevenson, after the two do battle in June.
But now a rematch before or around then appears to be the likely next step for both men, who struggled for the most part to captivate the crowd at the Echo Arena in a laborious encounter.
"I thought I won nine out of the 12 rounds and even Chilemba's trainer, Buddy McGirt, one of the most respected men in boxing, told me he thought I won," said Bellew.
"I've got a lot of time for Chilemba. He's a good fighter and a tough man but I won the fight."
The chief support bout also ended in a draw, but like in their first fight Derry Mathews and Anthony Crolla delivered the goods in their return bout.
Though a winner could not be decided by the judges at the end of their tussle for the vacant Commonwealth lightweight title, a third fight would go down well with the masses following two all-action affairs, with Mathews winning the first by TKO last year.