David Luiz was a welcome return for Arsenal as was Cedric Soares and reserve goalkeeper Runar Runarsson, who featured ahead of Bernd Leno.
Molde should've had a 14th minute lead from a ball across the centre of the area, but Runarsson reacted smartly to keep out an instinctive strike from Sheriff Sinyan.
Luiz looked to bring his side ahead following a looping header at the back-post after meeting a cross from the right-side, but went wide with Nicolas Pepe going close seconds prior.
Pepe had another chance to give Arsenal the lead from a surging run towards the area approaching the closing period of the first half, but fired wide following a cut inside.
Rob Holding replaced Luiz at the start of the second half, as the Gunners introduced the encounter's first substitution.
The Gunners cracked the underside of the crossbar two minutes from the restart following a thumping drive from Pepe after cutting inside.
Pepe wasn't to be denied on 50 minutes as the Ivorian international popped up on the right-side of the area to curl into the top corner from an acute angle.
Mikel Arteta's side did go on to grab a second 55 minutes gone as Reiss Nelson spotted a surging ball from the right by Joe Willock to apply a close-range finish.
The Norwegians' misery deepened eight minutes from time when Folarin Balogun got wind of a ball from the left to send in a bottom-low finish from inside the area.
Arsenal managed the closing minutes to claim victory and a spot in the knockout stages with two games to spare.