Alexis Sanchez clinically put Arsenal in front late in the first half at the Emirates on Wednesday night, latching onto an overhit pass which was intended for Jack Wilshere as the Gunners took the lead at a pivotal time.
Two penalty claims and a great deal of attacking intent meant the visitors were right to feel aggrieved to be behind at the interval, but the home side really should have put the game to bed with a host of second-half chances.
Their task was made all the more difficult however with 15 minutes to go as Mathieu Debuchy was sent off for a second bookable offence.
The visitors threw everything at Arsenal late on, but the Gunners showed their fighting spirit and held on to secure their place in the Champions League group stages for the 17th consecutive season.
The home side started brightly and had two great openings within the opening ten minutes. Wilshere did well to dart through an opening in the Besiktas defence, but the England midfielder dragged his shot wide.
Santi Cazorla was the next guilty party, looping the ball high and wide with an open goal gaping following a misplaced pass from Besiktas goalkeeper Tolga Zengin.
Two big penalty claims were waved away by Portuguese referee Pedro Proenca, with Wilshere especially fortunate to get away with a challenge on Ismail Koybasi.
Then, moments before half-time, came the crucial goal. Debuchy’s cross found its way to Cazorla on the edge of the box, who then played a neat one-two with Wilshere which was slightly overhit, but Alexis came in behind to finish.
After the interval, it was all Arsenal with several opportunities to make the game safe wasted by the hosts.
Sanchez was a metre away from making it 2-0 five minutes after the interval but he was beaten by the speed of Cazorla's pass and he should have done better moments later when set up by Wilshere.
Cazorla saw an effort blocked from close-range, before Alex Oxlade-Chamberlain also suffered the same fate from even closer in, with Zengin equal to his prod goalwards.
Moments later, Debuchy received his second yellow card, and the France full-back could face further sanctions for his reaction to the referee’s decision.
As a result, the Arsenal's defence could not rest as successive raids were met with scrambling responses.
The visitors almost broke the Arsenal faithful’s hearts in the dying moments as Demba Ba failed to connect with a pinpoint cross at the backpost, with Wojciech Szczesny scrambling to get across.
Arsenal held on and secure their place in the lucrative group stages, but with hitman Olivier Giroud seemingly out for a substantial period, a lack of firepower may have to be address by Arsene Wenger and the Gunners’ hierarchy.