Djokovic beat Marco Chiudinelli of Switzerland 6-4 6-2 in the second round and would have faced Mayer in the quarter-finals but the German pulled out with a hamstring injury after beating Tommy Robredo on Wednesday.
"It is never the best way to get a win like this and I feel sorry for Florian," Djokovic told reporters.
World number two Djokovic dominated on serve against Chiudinelli but needed more than a dozen break chances to see off the Swiss in a match lasting 90 minutes.
"I played conveniently and dominantly from the start on my own service game, and had many opportunities on his, however, I was less successful. I used the ones I needed." he added.
Russian second seed Nikolay Davydenko displayed a solid baseline game to overcome Marcos Baghdatis of Cyprus 6-3 6-2.
"Everything was good today about my performance, though I still don't feel comfortable on this surface and with the balls we are playing with," Davydenko told reporters.
Russian sixth seed Mikhail Youzhny beat Turkish qualifier Marsel Ilhan 6-4 6-4 to set up a quarter-final with Gael Monfils.
The Frenchman, seeded four, beat Dutch wildcard Thiemo de Bakker 6-3 6-2.