They will now face Champions League winners Mamelodi Sundowns in the Super Cup next February.
Mazembe, who had held their opponents to a 1-1 draw in Blida in the first leg of the final last weekend, went ahead after just seven minutes through Merveille Bope, reacting quickest to a free kick from Jean Kasusula which hit the woodwork.
Zambian international Kalaba hammered home a volley on the strike of half-time to make it 2-0 and scored again just after the hour mark to put the result beyond the Algerians, appearing in their first continental cup final.
Bejaija scored a consolation goal in the 75th minute from Sofiane Khadir but the three goal advantage was restored within 60 seconds by Jonathan Bolingi.
Mazembe, won 5-2 on aggregate, add the Confederation Cup to their list of honours after winning the African Champions League last year. They were eliminated early in defence of their trophy this year, dropping down to the continent’s secondary club competition.