His five penalties also matched the Lions record in South Africa held jointly by Neil Jenkins and Tony Ward. It was Ward's 18 points in South Africa in 1980 that Jones beat to set a Lions record.
The Lions' tally of 25 points was also the most they had scored in defeat against the Springboks, surpassing the 22 in the first Test in 1980, and was the third highest score they have ever recorded in any game against South Africa.
But the record was small consolation for Jones, who has now played in five successive Lions tests without tasting success.
"We are bitterly disappointed to lose. In the first half we were very good and I thought we had done enough to win," said Jones.
"We played some good rugby in the first half - we were accurate and efficient and put them under pressure and got some points.
"But you have to give them credit because they were very good in the second half. We gave everything, but it wasn't enough.
"They are the world champions and we were playing them at altitude in their own back yard. The game changed when it went to uncontested scrums and that made it a lot harder to attack and altered the dynamics of the game."
But Jones says there are no plans for the Lions to throw in the towel ahead of the third Test in Johannesburg.
"We have worked very hard throughout this tour. We set goals at the start and it is just a shame we haven't met them," said Jones.
"But we want to put pride back in the jersey and next week is all about doing the Lions jersey justice - that's our goal.
"We have given everything, but we have got one more opportunity. We will have to recharge our batteries.
"Whenever you play South Africa you expect it to be physical, but that was a step up again - right up there with the most physical matches I've ever played," said Jones.
"The collisions were massive. It was a really challenging match, a true test of your character and skill."