Ranked Africa's 13th-best side, Sierra Leone looked a much more impressive prospect than in their narrow 2-1 aggregate win against Swaziland in the previous round.
They are now heavy favourites to progress through the second round of qualification after two second-half goals put Seychelles on the back foot in the tie.
Khalifa Jabbie opened the scoring 11 minutes after the interval before Umaru Bangura double the hosts' lead from the spot at the National Stadium in Freetown.
It is advantage Botswana in their tie against Guinea Boissau as Lemponye Tshireletso's brace helped them to a 2-0 victory in Gaborone.
Botswana failed to qualify for the competition in 2013 but Tshireletso's first-half double edged them a step closer to the showpiece in Morocco ahead of their second leg.
Uganda also built on home advantage in Kampala to give them the upper hand in their tie with Mauritania.
After a goalless first half, the gap in quality began to show as goals from Brian Majwega and Geoffrey Massa helped the hosts to a 2-0 victory.
Uganda had been due to face Equatorial Guinea but saw their initial opponents banned from the competition for fielding ineligible Cameroon-born Thierry Fidjeu in their 3-1 aggregate win over Mauritania.
All three second legs will take place on August 2.
