Blackburn were denied victory by Marc Janko's late header in their Uefa Cup first-round first-leg tie.
Blackburn's Benni McCarthy is challenged by Remo Meyer
The game was stopped for six minutes because of floodlight failure but when it resumed Alexander Zickler put Salzburg ahead with a cool finish.
Robbie Savage immediately levelled with a curling free-kick and Benni McCarthy put Rovers ahead from close range.
Blackburn had further chances but substitute Janko equalised in the 92nd minute with a powerful downward header.
If they had held on, Rovers would have registered their first away European win after nine attempts, and only their second in 16 games against continental opposition.
Aware of his side's dismal record, Rovers boss Mark Hughes had elected to pack his midfield with McCarthy operating as a lone striker.
It was a tactic that worked and the home side were kept quiet in the opening minutes - until the floodlight failure at the hi-tech Red Bull Arena plunged the ground into semi-darkness.
When the game restarted, Salzburg quickly took the lead through German international striker Zickler, who slotted home his seventh goal in seven games on the half-hour mark after being fed by Christian Tiffert.
But Rovers responded just two minutes later, with Savage bending in a superb free-kick from 25 yards after David Bentley was fouled.
And before half-time Hughes' men were ahead.
Pedersen fired in a powerful free-kick that Timo Ochs failed to deal with and McCarthy showed his predatory instincts by winning the race to the loose ball and bundling it over the line.
More opportunities followed for Zurab Khizanishvilli and Bentley after the break before Savage wasted a golden opportunity to make it 3-1, ballooning Pedersen's pull-back over from eight yards.
Salzburg put on 6ft 5in striker Janko and elected for a more direct approach to try to get back into things - but they initially struggled to disrupt Blackburn's rhythm.
Eventually Niko Kovac's header did bring a fine save out of Brad Friedel with seven minutes left.
That set up a frantic closing period and Janko rescued a draw for his side when he met Kovac's deep cross with a header that Friedel could not keep out.
It was a disappointing ending for Blackburn but with two away goals they will still have the advantage in the second leg at Ewood Park on 28 September with a place in the group stage at stake.
Blackburn manager Mark Hughes:
"To lose a goal as late as we did has deflated us somewhat but I can't be too critical as I thought we were excellent.
"I thought tactically we were spot on and technically we dictated the play and had the outstanding performer in Tugay who I thought put on a masterclass.
"That¿s the disappointment because for long periods we were in control against a very good team and we made them look ordinary at times.
"It feels like a loss but two away goals puts us in good shape for the next leg."
SV Salzburg: Ochs, Bodnar, Dudic, Linke, Carboni, Kovac, Zickler, Jezek (Pitak 62), Tiffert (Vonlanthen 62), Meyer, Janocko (Janko 46).
Subs Not Used: Ozcan, Steinhofer, Aufhauser, Winklhofer.
Booked: Bodnar, Meyer, Carboni, Tiffert.
Goals: Zickler 30, Janko 90.
Blackburn: Friedel, Neill, Khizanishvili, Tugay, Emerton, Savage, McCarthy (Nonda 87), Bentley, Pedersen, Gallagher (Peter 81), Ooijer.
Subs Not Used: Brown, Todd, Mokoena, Jeffers, Nolan.
Goals: Savage 32, McCarthy 39.
Ref: Tomasz Mikulski (Poland).