The former Bristol City hitman – who goes by the nickname Jet – joined Livi just before the transfer deadline but has taken six weeks to open his account.
Livingston finish their Group H campaign with a perfect record of four wins from four and will be seeded for Sunday’s second-round draw.
And Emmanuel-Thomas is now aiming high as he chases further goals.
He told LFCLive: “They scored first which kind of gave us a rocket up the backside to realise that we actually do want the three points and to finish the group on top.
“The performance in the second half was a lot, lot better and it’s nice to get another win.
“I’m very happy (with the goals). It’s obviously been a long time coming. I’ve played in a lot of games and had a few chances where I could have opened the account but they never came. Today is the first and second of hopefully many.
“It’s about continuing with the confidence that comes from within myself and the team with the wins and hopefully we can keep pushing forward.
“It’s nice to be seeded in the next round so we’ll see who we get next but we’ve put ourselves in the best possible position to get a good draw in the next round.”