Having beaten the Danes in Copenhagen in June, the Croatians repeated the feat to reach 10 points from five games, one ahead of Denmark in their bid for a Nations League semi-final spot.
Defender Borna Sosa, who was born in the Precko district of Zagreb and learned his trade at local club Dinamo before moving to VfB Stuttgart, had opened the scoring by slotting home from the edge of the area four minutes after the break.
Despite Denmark's attack misfiring for much of the night, a moment of magic from Eriksen looked set to secure a point as he fired home a brilliant dipping shot in the 77th minute.
The relief was short-lived though as Majer, who came on for Mateo Kovacic after Eriksen's goal, picked up the ball on the edge of the box and rattled it past keeper Kasper Schmeichel.
Elsewhere in the Nations League...
It was a busy night in League C. In Group C3, Azerbaijan secured a late win over Slovakia. They had led for much of the game, and immediately replied to Erik Jirka's equaliser to take all three points.
In Group C1, Turkey came from behind three times to draw 3-3 with Luxembourg in Istanbul. Lithuania also draw 1-1 with Faroe Islands.
In League D, Andorra were 2-0 winners against Liechtenstein, with Moldova beating Lativa 2-1. Kazakhstan also beat Belarus 2-1, although Askhat Tagybergen was sent off late on for a second yellow card.
Lithuania and Belarus have now both been relegated to Group D.