"It's very disappointing," said McGeechan as the Boks fought back from a 19-8 deficit to break Lions' hearts with two converted tries and the same number of penalties in the closing stages.
"I thought the boys were outstanding, they got themselves in a winning position but they didn't quit finish it off.
"I was very proud of the performance and the whole attitude. No-one expected us to be so competitive. But with a little change of luck in both Tests, we could just as easily be stood here with two wins. That's how close Test rugby is."
The Lions dominated the first period at Loftus Versfeld but a raft of injuries disrupted their progress throughout the second half, as a make shift backline finished the game for the Lions after the match had gone to uncontested scrums with less than 50 minutes played.
McGeechan believes those setbacks clearly had an affect on the outcome of the match, although he admitted that the Lions perhaps could and should have put the game beyond the Boks.
"In the end we just ran out of players," added McGeechan.
"The sad thing is that there are significant injuries that we have to review but we're looking at the two props Gethin Jenkins and Adam Jones, Jamie Roberts and Tommy Bowe as well. Those injuries clearly disrupted the flow of a team that was playing very well.
"There were a couple of chances where we needed more composure to put them away and then we would have been out of sight by half time.
"We didn't make the best decisions in the second half and that caused us problems. We needed more territory and possession and we lacked the control we needed."