Under-strength Pau offered stubborn early resistance matching Blaine Scully's try with one by Daniel Ramsey.
Two scores by Cory Allen after the break, assisted by Steven Shingler, put Blues in the driving seat.
But the home team could not claim the bonus point score in the final 20 minutes, with centre Pierre Dupouy claiming a consolation try.
Blues will face second-placed Bath twice in December, with both teams unbeaten going into the first of those games in Cardiff on 10 December.
Blues coach Danny Wilson said: "I thought the boys played really well. We talked about the bonus point, but we had a good nine minutes I think it was of defending on our line.
"But you know what, that's probably better for us and where we are to have that real good shift of defence. Granted they they got over at the end but I think it shows some improvements in that area.
"And it showed boys fighting until the game was finished.
"It's nice when you can go out there and backs score three fantastic tries off first-phase, off solid set-pieces plays which is important and shows a mixture to our game."
Cardiff Blues: Dan Fish; Alex Cuthbert, Cory Allen, Garyn Smith, Blaine Scully; Steven Shingler, Lloyd Williams; Gethin Jenkins, Kirby Myhill, Taufa'ao Filise, Jarrad Hoeata, James Down, Macauley Cook, Ellis Jenkins, Josh Turnbull.
Replacements: Matthew Rees, Rhys Gill, Scott Andrews, Seb Davies, Kristian Dacey, Tomos Williams, Jarrod Evans, Matthew Morgan.
Pau: Charly Malie; Louis Dupichot, Bastien Pourailly, Pierre Dupouy, Marvin Lestremeau; Santiago Fernandez, Thibault Daubagna; Jérémy Hurou, Quentin Lespiaucq Brettes, Sylvain Charlet, Masalosalo Tutaia, Daniel Ramsay (capt), Pierrick Gunther, Sean Dougall, Ben Mowen.
Replacements: Lucas Rey, Geoffrey Moise, Joel Sclavi, Fabrice Metz, Giovanni Habel Kuffner, Thierry Lacrampe, Romain Buros, Baptiste Pesenti.
Referee: JP Doyle (England)
Touch judges: Wayne Barnes (England), Gareth Copsey (England)
Citing commissioner: Gordon Black (Ireland)
Attendance: 6,516
Cardiff Blues moved to the top of Pool 4 in the European Challenge Cup with a comfortable home win over Pau.