The most incredible result of the night, though, occurred at the Allianz Arena as Milner produced a starring performance for City as they came from two goals down to defeat Bayern Munich 3-2.
MORE: Manchester United return to winning ways with victory over Shakhtar Donetsk | Manchester City produce classic Champions League comeback
Both teams had already secured qualification from Group D and Manuel Pellegrini's decision to select second-string players such as Milner appeared to have backfired as the European and German champions overwhelmed his team in the opening stages.
Thomas Muller and Mario Gotze were on target to hand Bayern a 2-0 lead after 12 minutes, and City were fortunate not to be further behind as their defence flailed under the onslaught.
But they earned a route back into the match when David Silva marked his return from a calf injury by converting Milner's downward header and the same player won a penalty for Aleksandar Kolarov to equalise in the 59th minute.
Milner then netted a clinical finish as superb Spanish duo Silva and Jesus Navas unlocked a Bayern team who were improbably denied an 11th straight UEFA Champions League win.
Elsewhere in Group D, Viktoria Plzen secured qualification for the UEFA Europa League with a dramatic 2-1 home win over nine-man CSKA Moscow.
With Bayern Munich and Manchester City havng already progressed to the knockout stages of Europe's premier club competition, the Europa League spot was the only issue to be decided in the final round of Group D matches.
Pavel Vrba, who was taking charge of his final Plzen match before assuming control of the Czech Republic's national team, saw his side come from behind in dramatic fashion after Ahmed Musa's 65th-minute header put CSKA in front.
CSKA's Alan Dzagoev was dismissed for a clash with Vaclav Prochazka, and Plzen soon levelled through Daniel Kolar before Tomas Wagner scored a winner in the final minute of normal time.
There was also time for Pontus Wernbloom to be shown a red card as Plzen extended their European campaign into the new year for a third consecutive season.
In Group A, Manchester United finally found their fighting spirit as a 1-0 win over Shakhtar Donetsk secured top spot in Group A.
Under performing and under fire in the Premier League, David Moyes' men responded to their first consecutive home league defeats since 2002 with a battling display to progress to the knockout stages on a high.
Phil Jones' 67th-minute half volley ultimately proved the difference, but Shakhtar were left to rue what might have been as they controlled the action for long periods.
The Ukrainians failed to convert their chances - most notably Brazilian Alex Teixeira - as Bayer Leverkusen's 1-0 win at Real Sociedad sent them out.
Leverkusen, though, were made to work hard for their 1-0 win in Spain.
The Germans needed to produce a better result at Anoeta than Shakhtar Donetsk could manage away to Manchester United, and they did their bit with a battling away victory.
Leverkusen created the first half's better chances as a Gonzalo Castro free-kick hit the post and Simon Rolfes headed over, but Antoine Griezmann was presented with several opportunities of his own to give the Spaniards something to show for their efforts.
After a string of missed chances before the break for both sides, Omer Toprak finally prodded the visitors into the lead four minutes after the restart, while Stefan Kiessling headed against the crossbar.
The hosts attempted to push men forward towards the end as they sought their first home Champions League goal since December 2003, but Leverkusen held firm.
In Group B, Cristiano Ronaldo broke the UEFA Champions League record for goals scored in a group-stage campaign as Real Madrid beat Copenhagen 2-0.
The Portuguese superstar - who returned from a three-match absence with a thigh injury - scored three minutes after half-time at the Parken Stadium on Tuesday to take his tally to nine.
Real, who had already secured top spot, finish with 16 points from their six fixtures, while Copenhagen exit the competition and will also miss out on a Europa League berth.
After a slow opening Luka Modric sparked the match into life with a superb curling effort, but Carlo Ancelotti's charges survived a scare when Nicolai Jorgensen had an effort ruled out for an apparent handball.
The game was put beyond doubt when Ronaldo notched his record-breaking goal from just outside the six-yard box, and he missed the opportunity to make it 3-0 when having a penalty saved in the closing stages.
However, Group B is not yet fully decided as the final clash between Galatasaray and Juventus in Istanbul was postponed as a blizzard struck, forcing both teams off the field in the 31st minute.
The score at that stage was 0-0, although UEFA are yet to determine when this match – one that will determine the second team to advance from this group – is re-scheduled.
Olympiacos, meanwhile, qualified for the last 16 from Group C despite missing two penalties in a 3-1 victory over eight-man Anderlecht.
Javier Saviola put the hosts ahead shortly after the half-hour mark, before Sacha Kljestan pulled the Belgians level out of nothing before the break.
Saviola then saw his penalty saved four minutes into the second period, after Cheikhou Kouyate had been dismissed for a second yellow card, but made up for it by restoring Olympiacos' lead nine minutes later.
Substitute Vladimir Weiss had a chance to all but seal qualification in the 72nd minute, but found Silvio Proto in inspired form as the goalkeeper kept out another spot-kick, before Fabrice N'Sakala became the second Anderlecht player to be given his marching orders late on.
Remarkably, a third penalty was awarded and Proto dismissed for his foul on Weiss, and substitute Alejandro Dominguez kept his cool against stand-in keeper Aleksandar Mitrovic to wrap up the win.
The result sends the Greek side through due to their superior head-to-head record against Benfica, who triumphed over Group C winners Paris Saint-Germain.
Benfica, though, will have to be content with a Europa League position despite their excellent 2-1 victory over PSG.
It comes as a cruel blow to Jorge Jesus' men after they produced an excellent display against the Ligue 1 champions, recovering from Edinson Cavani's 37th-minute opener to claim the points on home soil.
Lima levelled with a first-half spot-kick, awarded following what appeared to be an accidental clash of heads between debutant Kalifa Traore and Silvio, before Nicolas Gaitan struck the winner 13 minutes into the second half.
But, despite inflicting PSG's first Champions League defeat in 14 matches, Benfica's inferior head-to-head record against Olympiacos saw their dreams of reaching the final, which will be hosted at their own ground, dashed.