In qualifying, during Q2, the Aussie got in the way of Alpine's Esteban Ocon, who was on a flying lap, forcing him to abort his lap.
The Ferraris of Charles Leclerc and Carlos Sainz secured P2 and P3 respectively while reigning champion Max Verstappen could only manage P4.
He was 1.4 seconds slower than Ferrari's Carlos Sainz's fastest lap and 0.6 seconds slower than new teammate George Russell.
The Monegasque driver set a best time of 1:29.735 to edge out defending world champion Verstappen by 0.033s.
On the soft compound tyres, Leclerc, who didn't break cover until halfway through the session, set a time of 1m 30.772s in the closing stages.
As per a report, a spokesperson for Red Bull said that the issues in both cars were due to a vacuum created in the fuel system.
Vettel, a four-time world champion, contracted COVID-19 ahead of the Bahrain GP last week and it seems like his recovery is not yet complete.
Hamilton won a highly contentious race at the Jeddah Corniche Circuit, with Horner claiming Mercedes' "spicy engine" gave them an advantage.
Hamilton and Verstappen are level on points heading into the final race, making the Abu Dhabi Grand Prix a winner-take-all event.
Hamilton passed Verstappen at the final corner on Lap 43 and pushed him wide at Turn 27, taking the lead and putting in the fastest laps.