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There was little to excite the small crowd in Egyptian city Ismailia until the five-time trophy-holders struck twice within three minutes midway through the second half.
Giant defender Yaya Banana nodded Cameroon in front on 66 minutes and forward Bahoken struck from close range three minutes later in Group F, which includes Benin and Ghana.
Cameroon were the fifth of the six top seeds after Egypt, Nigeria, Senegal and Morocco to win their opening match at the tournament while Tunisia were surprisingly held by Angola.
The Cameroon line-up included four starters from the 2017 final -- centre-backs Michael Ngadeu and Ambroise Oyongo, midfielder Arnaud Djoum and forward Christian Bassogog.
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Georges Mandjeck, who came off the bench during the 2-1 title-decider triumph over Egypt in Gabon, was also included by coach Clarence Seedorf.
For Suriname-born former Dutch start Seedorf the Cup of Nations represents a chance to improve his coaching credentials after flopping at clubs in Italy, China and Spain.
Before facing Guinea-Bissau, Seedorf had been in charge of nine Cameroon matches, winning three, drawing three and losing three.
The best chance of a goalless, uninspiring opening half at the Ismailia Stadium came after 31 minutes when Bassogog ballooned wide a Karl Toko Ekambi cutback.
It was a deeply embarrassing moment for the 2017 Cup of Nations winner, who should at least have been on target with the Guinea-Bissau defence disorganised.
Earlier, Judilson Gomes went close to giving the Guinea-Bissau Djurtus (wild dogs) the lead with a fierce snap shot that finished narrowly off target.
After Bassogog fluffed his chance, Cameroon created another opening from a free-kick and Guinea-Bissau goalkeeper Jonas Mendes parried a Joyskim Tchakonte header to safety.
The second half was meandering along with no hint of a goal until Cameroon netted twice within three minutes to swing the match in their favour.
From a corner, Banana soared in the middle of the goalmouth to nod powerfully into the net off Guinea-Bissau defender Rudi Silva.
The goal ratted the outsiders and they fell further behind when a cross struck a defender and fell invitingly for Bahoken to fire past Mendes.
Later Monday, the second match of a doubleheader pits four-time champions Ghana against a Benin side seeking a first Cup of Nations victory after eight losses and a draw.