Spain's Guillermo Garcia-Lopez, the world number 77, proved too strong for Evans, recovering from a mid-match blip to win 6-4 1-6 6-1.
Evans, 21 and from Birmingham, is due to play singles in Britain's Davis Cup tie against Slovakia in Glasgow next week in the absence of Andy Murray, who is unavailable due to minor injury concerns.
The youngster showed encouraging form in beating Canadian Frank Dancevic, Croatian Franco Skugor and Swiss player Stephane Bohli to come through qualifying in Zagreb.
However, Garcia-Lopez had the stamina to get past him in their clash, getting on top of the Evans serve from the early stages and showing superiority in the deciding set.
British number five Evans, ranked 296th in the world, has not played in the Davis Cup since losing both his singles matches in the defeat by Lithuania in March 2010.