Police are questioning them in connection with the blasts at BJP leader Narendra Modi's poll rally in Patna last month and also the explosions at Bodh Gaya in July.
Mohammed Saeed Abdul Jaleel (50) and Azharuddin Samshuddin Qureshi (19) were apprehended last evening, a senior officer said.
"Jaleel, a resident of Sanjay Nagar area, and Qureshi of Rajatalab locality were nabbed for their alleged links with the banned terror outfit," Raipur SP OP Pal told PTI.
With the arrest of the duo, the number of activists linked to the Student Islamic Movement of India (SIMI) held from Chhattisgarh so far, has reached 13, he said.
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Police said Jaleel was running a medical shop at Baijnathpara here. "Azharuddin discontinued his studies and was reportedly participating in camps organised by Siddiqui," the SP said.
"More startling disclosure would come up further as the investigation progresses," he added.
Police had apprehended Sidhhiqui, who runs a coaching centre in Raja Talab, and auto driver Abdul Wahid Khan (54) of Pandri area on November 14 for their alleged links with SIMI.