It was a cruel end to a campaign that McGeechan had hoped might bring another series triumph to go alongside the one he achieved as a player in 1974 and the two he won as a coach in 1989 and 1997.
But while the Lions fell to Morne Steyn's cruel kick, McGeechan said he was still full of pride at the way his players had performed in both Durban and Pretoria. He feels it could have been a totally different story if the Lions had had the rub of the green.
Here are some of his thoughts on the series to date:
MCGEECHAN ON WHAT THE LIONS HAVE ACHIEVED
We have just watched one of the best Test matches the Lions have played. That is because the attitude was so positive and so focused on producing a game that I am very proud of being associated with. We have had two cracking Test matches. People say 'are the Lions still valuable?' The rugby we have played has been outstanding and has been a great advert for the players in the northern hemisphere because we have seen some of the best rugby ever.
ON THE SECOND TEST AND THE SERIES
We wanted to make sure we were able to play the rugby we wanted to play and that comes from not being afraid of the contact. We certainly weren't afraid and the game was as physical as it was partly because of our approach.
I don't think uncontested scrums helped us because we were working the big Springbok forwards in more than one way and it becomes a soft platform. Losing the two props together was a massive blow and I think the game would have been different if they had stayed on.
Last night was probably as low as I have felt for a long time in my career because I know how much had gone into that game and how much it meant to the players. The look in that dressing room at the end - there was a lot of sadness there.
I am just disappointed we are not sitting here at 1-1 in a Test series or even 2-0 up because I think the players genuinely deserve to be in that position. I probably didn't say enough to the players. It was only when I started getting messages from back home, with people talking about some of the best Lions rugby they have ever seen. They understand they have been part of a quite fantastic series.
I wouldn't change anything I have done up to this point, with the planning, the management, the way we operate, the way we train, the tactics because in the end it was just the rub of the green that has not given us one or two results.
I am hugely proud of what has been achieved and we will take that into the third Test.
I have always respected South African rugby and I think Lions Tests in South Africa remain the ultimate challenge for players.
ON CREATING SOMETHING SPECIAL ON TOUR
I think this has been as good an atmosphere on a Lions tour as I have ever experienced. I think South Africa have seen this series as being as big as, if not bigger than, their World Cup win. If anyone asks 'what do the Lions mean?' they have probably only got to ask the Springboks.
Five, six, seven of them traveled back to South Africa to be part of this series. There is more emotion in some of these games than they would ever find in a Tri-Nations game.
ON THE LIONS' FUTURE
We have restored a lot of credibility to the Lions on this tour. In our disappointment, probably one of the things I should have done yesterday was take the team out to thank the supporters. We will certainly do that next week because the support has been quite incredible. To me, the Lions have just got bigger in other people's eyes.
Unless you have been associated with the Lions you don't realise the impact they make. I just wish more of those people who don't want to make time for the Lions would come out and experience a Lions tour because I don't think they understand the impact. For the players they represent they should make it work.
For the professional player, this is what he wants to do. This is where he wants to be. This is the shirt he wants to wear. Going forward, we have got to make that easier to happen. By doing that you make the preparation easier to win a Test series. That is to everybody's advantage. Whether it is Australia, New Zealand or South Africa, give the Lions a fair crack.
The Lions have been very special to me over a huge number of years and I would be very sad if the Lions were not part of the international calendar going forward. I don't think that is a danger. The important thing is to get everyone to agree that in a Lions season, just as in a World Cup season, you make adjustments to the season for the players. It is those people who I think need to come on a Lions tour and understand the impact of what it means.
There will be a report going in on what we have done and how we have done it. There are probably things you need to have in place as a minimum to have a fair crack. Some of those have to take in the structure of the season in the northern hemisphere. You probably want slightly more sympathetic views towards the Lions at key times.
The two biggest things in the international calendar are World Cups and Lions tours. If we could respect that then I think that preparation can help the next coach.