The Dons survived some early pressure in their second qualifying round first-leg match before goals from defender Andrew Considine, midfielder Peter Pawlett and substitute Kenny McLean put them in the driving seat ahead of the return game at Pittodrie.
However boss McInnes, despite praising his players to the hilt, also urged caution ahead of the second leg next week.
“I was immensely satisfied and proud of the players’ efforts,” he said.
“The conditions were very difficult, the Rijeka supporters stayed with their team and they kept trying to ask questions of us but we got goals at good times which gave the players a lift and I thought we were very smart with our work.
“Our players were excellent in terms of their application and what we asked of them but that is the only part of the game, tactics and organisation.
“The sheer endeavour and effort the players put in was very pleasing to see for me and very rewarding.
“But it is still only half-time in the tie. It doesn’t mean to say we can’t feel good about ourselves for tonight’s work but they are too good a team to think the tie is over.
“There is work to do still. Yes, we will enjoy tonight, we will feel satisfied with our work but the preparation for next week’s game starts now.”
McInnes also praised travelling Dons fans and said: “I thought our own support were fantastic, you could hear them throughout the game and I thank them for the effort they made to come here and get behind the team.”