In 2009, Steyn landed a late penalty from his own half to give the Springboks an unassailable 2-0 lead in the series they also won 2-1.
Now 37, Steyn replaced fly-half Handre Pollard with 15 minutes remaining and almost immediately slotted a penalty to give the Rugby World Cup winner a 16-13 advantage.
Rival fly-half Finn Russell, an early replacement for the injured Dan Biggar, levelled with his third penalty of the match five minutes from time.
Then, with one minute remaining in a tense tussle, the Springboks were awarded another penalty and Steyn calmly scored to edge the hosts ahead again.
The drama was not over, though, as the Lions were awarded a scrum inside South African territory, offering them a chance to snatch a dramatic victory.
However, it was not to be as the tourists were penalised at the set piece, Steyn booted the ball into touch and French referee Mathieu Raynal signalled the end of the match.
It was the first appearance by Steyn in the green and gold jersey since 2016 and he raised his Test points total to 742 from 67 caps.
The Lions opted to kick for touch three times in the first half and once in the second when awarded penalties in kickable positions.
They scored the first time after winning the lineout, but failed to secure points on the other three occasions, leading to a ninth series loss in 14 attempts against South Africa.
“It was crazy to have a game this big and to have an empty stadium. But it does not take away from what this team has done,” said Springboks captain Siya Kolisi.
“It has been a very tough series. We all wanted it. We know how much it means to the country. Both teams gave it everything they had.”
South Africa were severely hampered by not being able to play for 19 months due to the coronavirus pandemic after winning the World Cup in Japan.
They began the series against the Lions having played just one warm-up match, which they won comfortably against second-tier opponents Georgia.
It was an historic series victory as no team has succeeded in the 130-year rivalry between South Africa and the Lions after losing the first Test.
The Springboks went down 22-17 in the opener this time and hit back with a 27-9 triumph last weekend to level a series played behind closed doors because of an ongoing third wave of Covid-19 in South Africa.
Winger Cheslie Kolbe scored the lone home try after evading full-back Liam Williams and hooker Luke Cowan-Dickie and Pollard converted to put the home team 13-10 ahead after trailing by seven points at half-time.
The rest of the Springbok points came from four penalties with Pollard, who finished the match on 502 Test points after missing two shots at goal, and Steyn slotting two each.
Hooker Ken Owens claimed a pushover try for the Lions and Russell, kept out of the team by an ankle injury since July 7, contributed 11 points from a conversion and three penalties.
“We are really disappointed. We gave away a couple of silly penalties towards the end,” said Lions skipper Alun Wyn Jones, who made a remarkable recovery from a shoulder injury to play in all three Tests.
“But to put it into perspective, we are fortunate to be here, to represent the Lions and play the sport we love.
“Many people have had it tougher. We are very conscious of what we represent.
“(I want to compliment) the Springbok set piece and game management.”