Hamilton's best effort of one minute and 20.802 seconds saw him finish 0.090 secs ahead of Bottas - a victor last time out in Russian Federation - with Kimi Raikkonen leading Ferrari's effort in third and Vettel trailing only in fourth.
Valtteri Bottas was extremely close behind his team-mate on both occasions-just 0.029 and 0.090 seconds, respectively, in fact-while Kimi Raikkonen and Sebastian Vettel of Ferrari followed the Silver Arrows pair in Catalunya, with the latter missing part of the first session because of gearbox problems with his auto.
Red Bull, despite bringing a host of new parts to Spain, remain the third best team - albeit closer to both Mercedes and Ferrari - with Max Verstappen and Daniel Ricciardo fifth and sixth in the order.
Sebastian Vettel says F1 upgrades are about quality, not quantity, after seeing Mercedes' heavily-revised W08 challenger dominate Friday practice ahead of the Spanish Grand Prix.
"Today was an important one for us with the new upgrade package on the auto", he said. I think we are all learning as we go from race to race and I think for some cars perhaps it works immediately than for others. "It's a good feeling for everyone when these upgrades work".
Sebastian Vettel refused to deny he has had talks with Mercedes over a move to join Formula One's world championship-winning team in 2018.
"It's been a much better start to the weekend for me than in Sochi so I'm very happy".
"It's not my decision but I'm ready to race whoever comes along".
Kimi Raikkonen, who at the moment is virtually fighting for his long term Grand Prix life at Ferrari, is the holder of the lap record at Catalunya set way back in 2008 in his normally aspirated Ferrari (time 1m 21.67s).
"I really enjoyed it out there so I hope we can squeeze more performance out of the package". "There will be upgrades for everybody and we will be doing work tomorrow to get the auto in the right place".
Ferrari and Mercedes may be the front-runners again, but Red Bull expect to be close in pursuit with a heavily-updated vehicle while local hero Fernando Alonso has more modest hopes.
"And I think it's a very good challenge to try and beat them".
Felipe Massa was ninth for Williams, while Carlos Sainz Jr completed the top 10, having caused a brief red flag an hour in when his Toro Rosso shed debris after running over the exit kerbs at Turn 9.
In news from the back of the pack, Sauber have agreed a deal with Honda to run their engines from next season. "Very tricky conditions today", said Raikkonen.