Eduardo, out since last February following a horrific leg injury, set up a close-range finish for Niko Kranjcar, another long-term casualty making a successful international return.
"It was easy to score after Eduardo's perfect assist, we all knew he would be back with a roar. We all believed in him and we are all aware how much stronger we are with him," Kranjcar told reporters.
"The win will give us a new impetus ahead of testing World Cup qualifiers," the Portsmouth midfielder added.
Croatia are five points behind leaders England in Group Six and without Eduardo they have struggled to reproduce the attacking flair which propelled them through Euro 2008 qualifying, during which the Arsenal striker scored 10 goals.
He was absent from the finals in Austria and Switzerland after suffering a fractured fibula and an open dislocated ankle during last season's Premier League match at Birmingham.
The Croatians, who reached the last eight and were knocked out by Turkey on penalties, missed his lethal finishing in the tournament.
They have found it equally hard to score in World Cup qualifying without Eduardo and their lack of bite up front was particularly obvious in a 4-1 home drubbing by England and a tepid 0-0 draw in Ukraine.
Coach Slaven Bilic acknowledged the 25-year-old striker, who has scored 13 goals in 22 international appearances, would be a major boost to his side hoping to reach their fourth successive World Cup as an independent nation.
"I am delighted to have Eduardo back and his return is an enormous bonus for us," said Bilic.
"His ball control, the ability to hold it and wait for support has been sorely missed and it makes all the difference when we play top-level opposition."
Croatia are away to Andorra in their next qualifier on April 1, when England host Ukraine at Wembley.
