The Glamour Boys bounced back from their 1-0 defeat to Kenya Police in their previous outing to collect all three points, while Mombasa United's search for their first league victory of the season continued.
The visitors took the lead in the 44th minute through Brian Ogutu, who produced an impressive individual effort, dribbling past three defenders before finding the back of the net to give Shabana a 1-0 advantage heading into the break.
Shabana doubled their lead shortly after the restart when Kevin Omundi capitalised on a defensive error from the hosts. Brian Michira provided the assist after initiating a quick counterattack that exposed Mombasa United's defence, allowing Omundi to make it 2-0.
However, Mombasa United responded through Dennis Mabeya, who converted from the penalty spot after George Onyango was penalised for a high boot on Adeyemi Mogbademu inside the box.
The hosts continued to push forward and eventually restored parity when Waziri Junior rose highest to head home a corner delivered by Angal, bringing Mombasa United back into the contest at 2-2.
Having surrendered their two-goal advantage, Shabana needed a response, and it was substitute Derrick Oketch who stepped up in the closing stages.
The forward took advantage of sloppy defending from Mombasa United in the 82nd minute to fire past the goalkeeper and restore Shabana's lead, sealing a crucial 3-2 victory for the visitors.
The result takes Shabana to nine points after six matches, providing a timely boost following their previous defeat, while Mombasa United remain at the bottom of the 18-team standings with just one point from their opening six fixtures.
The newly promoted side will be disappointed to have surrendered their comeback after fighting back from two goals down, as their wait for a maiden SportPesa League victory continues.
Starting Lineups
Mombasa United: Mustapha Oduor, Ramadhan Hamisi, Ahmed Abdullahi, Hakimu Msami (C), Dennis Mabeya, Brian Odhiambo, Peter Abiola, Rodgers Oporia, Neville Getarale, Laban Otieno, Adeyemi Mogbademu.
Shabana FC: Pavel Ndzila (GK), Brian Bett, Kevin Omundi, James Mazembe, George Onyango (C), Biron Otieno, Herbert Sanday, Brian Michira, Sigmun Maina, Brian Ogutu, Hafiz Alhassan.
