Still the Blues came back, though, Frank Halai, George Moala and Benji Marshall scoring tries to set up a thrilling finish.
The Blues' five tries and close margin of defeat earned them two bonus points so they at least earned something tangible from their South African trip, but the failure to impose themselves on the Lions early was costly, something skipper Luke Braid acknowledged afterwards.
"We've had a problem with that,'' he said after similar starts against the Highlanders, Crusaders and Bulls. "To our credit we came back strongly but two yellow cards and 20-0 down, it's hard to come back from that.
"As a team we've got to learn to get tougher and play more clinically when the going gets tough.''
Kirwan's decision to play Marshall at fullback and move Piutau to the wing after the loss to the Bulls had mixed results.
Marshall scored a good individual try at the finish, but looked mostly tentative. An attempted clearance was charged down in the second half which led to more points for the Lions.
Piutau worked his way into the game but seems wasted on the wing. Another decision Kirwan must ponder on the flight home is whether to start halfback Bryn Hall over Piri Weepu against the Cheetahs at Eden Park. Hall was superb when he came on in the second half, scoring a try and making the long break from deep which led to Halai's.
Noakes did little to suggest he is a better option than Simon Hickey at first-five, while Pita Ahki and George Moala failed to convince as midfield partners. The Blues are likely to welcome in All Black Ma'a Nonu for the match against the Cheetahs.
The problems at Ellis Park started in the pack though, with only Faumuina and Patrick Tuipulotu, who went off in the first half with a leg injury, impressing. The scrum was pushed around by the Lions, a tighthead conceded on attack. There is attacking potential to burn in the backline but the inability of the forwards to put them on the front foot remains a weakness.
Lions 39 (Faf de Klerk, Coutnall Skosan, Coenie van Wyk tries; Marnitz Boshoff 3 cons, 4 pens, 2 dropped goals)
Blues 36 (Charles Piutau, Frank Halai, Bryn Hall, George Moala, Benji Marshall tries; Chris Noakes 2 cons, pen, Simon Hickey 2 cons)
Halftime: 17-0