The hosts showcased their attacking flair and defensive resolve to set up a showdown with Angola, who earlier thrashed Madagascar 4-1.
Coach Vela Khumalo made one tweak to the side that drew 0-0 with Mauritius, recalling Orlando Pirates' midfield maestro Kabelo Dlamini for Vuyo Letlapa.
Bafana wasted no time asserting dominance, striking in the eighth minute when Kamogelo Sebelebele's cross forced Comoros' Idris Mohamed into an own goal.
Six minutes later, Mamelodi Sundowns' Boitumelo Radiopane doubled the lead, latching onto Gape Moralo's through ball and firing off the post for his first tournament goal.
Comoros fought back, with Ibrahim Madi pulling one back on the half-hour mark, cutting in from the back post to drill a low shot past Kaizer Chiefs' goalkeeper Bontle Molefe.
The Coelacanths pressed for an equalizer, but Bafana's defensive unit, led by Stellenbosch FC's stalwarts, held firm. Dlamini nearly restored the two-goal cushion before halftime, his curling effort rattling the upright.
The second half saw Khumalo replace Dlamini and Mduduzi Shabalala with Letlapa and Masindi Nemtajela. Comoros persisted but struggled to breach Bafana's deep-lying defence.
In the 78th minute, Sebelebele sealed the deal, pouncing on a loose pass to fire home from close range to make it 3-1.
Late changes saw SuperSport United's Yanda Mfolozi and Victor Letsoalo replace Puso Dithejane and Radiopane.
Comoros' hopes faded when Naimoudine Assane was sent off in the 80th minute for a second yellow.
Bafana managed the closing stages comfortably, securing their final berth.
Bafana now face Angola on Sunday, aiming to reclaim the COSAFA crown before a passionate home crowd.
Bafana Bafana forward Percy Tau has responded to growing criticism over his recent performances and absence from the national team, insisting he still has a significant role to play in South Africa's football plans.
Kaizer Chiefs' Thabo Cele admits he is desperate to overcome his recent injuries and turn out for Bafana Bafana.
Bafana Bafana suffered a 3-0 defeat to Angola in the final of the COSAFA Cup at the Free State Stadium on Sunday.
Bafana striker Fagrie Lakay has won the Egyptian League Cup with Ceremica Cleopatra.
