The Dons may even have won after Niall McGinn put them ahead with just 11 minutes remaining against Shkendija at the Philip II Arena.
But substitute Hristijan Kirovski levelled just five minutes later to ensure the tie is finely poised going into the second leg at Pittodrie next Thursday.
There was a further setback for the visitors when it emerged Scotland squad defender Mark Reynolds suffered a suspected broken shoulder in the second half.
McInnes was disappointed to concede but remained content with the final result given his squad are still finding their feet following a recent return to pre-season training.
Croatian side Rijeka lie in wait in the second preliminary phase and the SPFL Premiership outfit’s coach is optimistic in is his men who will be bound for the Adriatic coast.
McInnes said: “I believe we can get through to the next round but the game is still very much in the balance. We know we will have to put in a strong performance in the second leg.
“I always felt the game would be over the two legs and we would have to be good over two games so we have work to do but we are still confident. We aim to improve next week.
“You are never totally satisfied if you don’t win the game but I felt it was a decent performance from us. I felt we were comfortable in the game
“They are a good side. I thought they were a good side before and I still think they are a good side. We were comfortable without producing a top performance and there is still work to do.”