Felipe Massa's morning benchmark was enough to ensure Ferrari ended on top on a day when reigning world champion Sebastian Vettel got his first taste of Red Bull's RB9.
The Brazilian set the fastest time seen so far this week at Jerez when he broke the 1m18s barrier during a short run on soft tyres.
His 1m17.879s wasn't threatened in the afternoon, with only Nico Rosberg in the Mercedes W04 able to get within one second of the time.
Three different cars - McLaren, Lotus and now Ferrari - have topped the opening three days.
Rosberg provided a welcome relief to the setbacks Mercedes had suffered on days one and two by racking up 148 laps, comfortably the most of any driver.
The German had been forced to cut short his day one programme due to electrical issues, while a rear-brake issue caused Hamilton's debut test for Mercedes to end early and in the barriers.
Vettel also broke into triple figures in the lap count, while an afternoon improvement was enough to send him into third overall.
Kimi Raikkonen, like Vettel getting his first taste of his team's 2013 car, improved in the afternoon session and finished just over one tenth of a second down on the triple world champion.
On his first day in the Toro Rosso STR8, Jean-Eric Vergne finished fifth, just ahead of Force India's simulator driver James Rossiter.
Rossiter managed 42 laps in the morning before handing over to Paul di Resta, whose programme was then derailed after just seven laps due to an exhaust issue.
Jenson Button, who brought about a premature end to the day when he stopped out on track between Turns 7 and 8, was seventh ahead of Sauber's new signing and F1 rookie Esteban Gutierrez.
The Mexican was the day's second busiest driver with 110 laps.
Several late improvements helped carry Max Chilton into ninth, above Williams's new signing Valtteri Bottas and Caterham's Charles Pic.
|Position||Driver || Team||Time||Laps|
|2.||Nico Rosberg||Mercedes||1m18.766s +0.887||148|
|3.||Sebastian Vettel||Red Bull||1m19.052s +1.173||102|
|4.||Kimi Raikkonen||Lotus||1m19.200s +1.321||40|
|5.||Jean-Eric Vergne||Toro Rosso||1m19.247s +1.368||85|
|6.||James Rossiter ||Force India||1m19.303s +1.424||42|
|7.||Jenson Button ||McLaren||1m19.603s +1.724||83|
|8.||Esteban Gutierrez||Sauber||1m19.934s +2.055||110|
|9.||Max Chilton ||Marussia||1m21.269s +3.390||78|
|10.||Valtteri Bottas||Williams||1m21.575s +3.696||86|
|11.||Charles Pic ||Caterham||1m22.352s +4.473||57|
|12.||Paul di Resta||Force India||1m23.729s +5.850||7|
All Timing Unofficial