The best fly-half in the world ceded the place-kicking duties to inside centre Tom Taylor, who succeeded with five of six shots at goal before a small Ellis Park crowd given the seven-time champions were in town.
But Carter, sidelined by a groin injury during the triumphant march of New Zealand to the World Cup title at home last October, played a role in both Crusaders tries.
As the visitors menacingly moved the ball wide on 31 minutes, Carter reversed the flow with an inside pass to left wing Zac Guildford, who caught the Lions defence napping as he sprinted over for a try.
Taylor converted to give Canterbury an undeserved 10-6 lead as the Lions had been the dominant force and they finally made advantages in territory and possession tell when prop Patric Cilliers dived over for a try.
Fly-half Butch James added the extra points for a 13-10 half-time lead the Lions lost three minutes after the break when Carter was involved in a handling move that ended with Sean Maitland racing on to a grubber kick and scoring.
Taylor converted again and added two penalty goals, while James was well off target with a stoppage-time penalty attempt that he needed to score from to give the Lions the bonus point that their perspiration warranted.
Carter, who came off the bench in a victory over South African visitors Central Cheetahs in Christchurch last weekend, quit unharmed on the hour mark, with Ryan Crotty taking his place.
Another All Blacks icon, injured captain and flank Richie McCaw, has yet to play this season, but in his absence, the likes of man of the match Kieran Read and fellow back-row forward George Whitelock impressed.
"It was a really hard game and we had to dig deep in the second half to gain the ascendancy," admitted a smiling but breathless skipper Read, after a match staged 1,800 metres above sea level.
"We got close but not close enough," confessed Lions captain and flank Josh Strauss. "After a good first half we let ourselves down in the early stages of the second half."
Taylor kicked three penalties and two conversions for the visitors, who were winning for the third time in five outings, while James kicked two penalties and a conversion for a Lions team suffering their fourth consecutive loss.
CRUSADERS 23 (Zac Guildford, Sean Maitland tries Tom Taylor 2 cons 3 pens) btLIONS 13 (Patric Cilliers try Butch James con 2 pens) at Ellis Park.