No, they've never appeared together on-screen before.
The first character mentioned in the question has appeared in the following episodes:
- Terror of the Autons
- The Mind of Evil
- The Claws of Axos
- Colony in Space
- The Daemons
- The Sea Devils
- The Time Monster
- Frontier in Space
- The Deadly Assassin
- The Keeper of Traken
- Logopolis
- Castrovalva
- Time-Flight
- The King's Demons
- The Five Doctors
- Planet of Fire
- The Caves of Androzani (as a hallucination)
- The Mark of the Rani
- The Ultimate Foe
- Survival
- The TV movie
- Utopia/The Sound of Drums/Last of the Time Lords
- The End of Time
-
Most episodes of series 8, as Missy
- The Magician's Apprentice
The second has appeared in the following:
- Genesis of the Daleks
- Destiny of the Daleks
- Logopolis (as a hallucination)1
- Resurrection of the Daleks
- Revelation of the Daleks
- Rememberance of the Daleks
- The Stolen Earth/Journey's End
- The Magicians'sMagician's Apprentice
As you can see, there are only two episodes common to both characters: The Magician's Apprentice, which is the episode under consideration, and Logopolis. However, one of our two characters only appeared as a hallucination of the Doctor, and didn't share any screen time with the other.
Although I'm not excessively familiar with the Doctor Who expanded universe (by which I mean the various novel series, comics, and audio productions), a quick skim of the two characters' pages on the TARDIS Data Core (the Doctor Who wikia)the TARDIS Data Core (the Doctor Who wikia) indicate that they haven't met in any of them, either.
1 Hat tip to Elliott Frisch for reminding me of this in comments