Sri Lanka, who'd already beaten Middlesex, won on the fourth and final day after being made to follow-on.
England Test call-up Eoin Morgan and Ravi Bopara, left out of the 12-man squad named earlier Sunday for the first of a three-Test series starting in Cardiff on Thursday, both fell victim to paceman Fernando, who finished with figures of three for 33.
Nuwan Pradeep took four for for 29 as Sri Lanka bowled out the Lions for 183 in the hosts' second innings.
Earlier the Lions dismissed Sri Lanka for 448, featuring hundreds from captain Tillakaratne Dilshan and Tharanga Paranavitana, with Surrey's South Africa-born Jade Dernback taking a career-best nine wickets in the match. That left the Lions needing 222 in 73 overs for victory.
But the target proved beyond them with Morgan, whose 193 in the first innings cemented his Test place, falling for just four second time around when he was caught low down at second slip.