The Dane had set the pace after dipping into the 1m 23s bracket courtesy of a stint on Pirelli's red-marked supersoft tyre, but with around 30 minutes of the morning to run Hamilton - shod on the yellow-marked softs - improved to a 1m 23.622s.
That lap was around six tenths of a second slower than Nico Rosberg's morning benchmark from day one - which was also set on softs - but was still enough to keep Mercedes on top for the third session running.
The Silver Arrows were also the class of the field in terms of lap count, with Hamilton completing 73 in total.
Behind Magnussen, Sebastian Vettel - the morning's second busiest runner - booked third for Ferrari, the four-time world champion having spent the majority of his time focusing on various medium-tyre runs.
Valtteri Bottas was fourth for Williams, while McLaren completed another encouraging morning as Jenson Button clocked 45 laps and wound up fifth fastest, 0.032 down on Bottas.
The morning wasn't quite so smooth for Haas or Sauber, who were both waylaid by technical issues.
The former were restricted to just one solitary installation lap after they discovered 'an unexpected anomaly' following an overnight turbo change, which followed a disrupted first day in which Esteban Gutierrez managed just 23 laps in total.
Sauber meanwhile also lost much of the morning, with Marcus Ericsson returning just before the lunchbreak to set his first timed laps of the day and take his overall count to seven laps.
Red Bull focused on pit stop practice rather than lap times early on, with Daniel Ricciardo eventually winding up sixth fastest, fractionally faster than Toro Rosso's Carlos Sainz.
Force India's Sergio Perez and Manor's Pascal Wehrlein completed the top nine, ahead of the errant Sauber and Haas drivers.
Wednesday morning's unofficial testing times from Barcelona
| POS | Driver | Team/Car | Best lap | Gap | Laps |
| 1 | Lewis Hamilton | Mercedes F1 W07 Hybrid | 1:23.622 | 73 | |
| 2 | Kevin Magnussen | Renault R.S.16 | 1:23.933 | 0.311 | 56 |
| 3 | Sebastian Vettel | Ferrari SF16-H | 1:24.611 | 0.989 | 63 |
| 4 | Valtteri Bottas | Williams-Mercedes FW38 | 1:25.151 | 1.529 | 57 |
| 5 | Jenson Button | McLaren-Honda MP4-31 | 1:25.183 | 1.561 | 45 |
| 6 | Daniel Ricciardo | Red Bull Racing-TAG Heuer RB12 | 1:25.235 | 1.613 | 42 |
| 7 | Carlos Sainz | Toro Rosso-Ferrari STR11 | 1:25.300 | 1.678 | 59 |
| 8 | Sergio Perez | Force India-Mercedes VJM09 | 1:26.188 | 2.566 | 58 |
| 9 | Pascal Wehrlein | Manor Racing-Ferrari MRT05 | 1:27.064 | 3.442 | 42 |
| 10 | Marcus Ericsson | Sauber-Ferrari C35 | 1:30.309 | 6.687 | 7 |
| 11 | Esteban Gutierrez | Haas-Ferrari VF-16 | - | 1 |
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