Test call-up Eoin Morgan and Cardiff reject Ravi Bopara were among the victims as Fernando (three for 33) took three wickets for four runs and then Pradeep (four for 29) completed the job to help Sri Lanka bowl the Lions out for 183 at Derby.
The hosts, who had enforced the follow-on on Saturday, bowled Sri Lanka out for 448 yesterday morning on the back of Jade Dernbach's career-best nine-wicket haul to leave themselves needing an apparently routine 222 in 73 overs for victory.
But Fernando, taking advantage of a strong wind behind him, produced a testing mid-afternoon spell to see off first James Taylor and then the Lions powerhouse pair at number three and five.
The Lions had taken just 14 overs between the showers on the final morning to get through the Sri Lanka tail, from an overnight 392 for six.
But when Tillakaratne Dilshan introduced his own off-spin early in the home reply, it was too much for Jimmy Adams - lbw pushing forward.
Taylor and Bopara dug in after lunch until Fernando started to work over the opener with pace and bounce.
Pushed back in the crease, Taylor failed to cover any movement when he pushed forward at one that trimmed the off bail.Then Fernando bagged Bopara and Morgan in the same over, the former unable to get his gloves out of the way of a devilish short delivery which followed him and the latter pulling his first ball for four only to edge his second low to second slip.
Samit Patel and James Hildreth appeared to put the Lions back on course in a stand of 61. But Patel was unable to cash in significantly before Pradeep pinned him lbw on the back foot. When captain Hildreth's was the third of three more wickets to fall in three overs for just six runs, Dinesh Chandimal taking a catch at deep midwicket off Pradeep with more than 60 runs still needed and eight down, the game was up.