The Briton, who has not won at Silverstone since 2008 but desperately needs to do so on Sunday to rein in runaway team mate and Formula One championship leader Nico Rosberg, set a best time of one minute 34.508 seconds on a blustery day.
However, Hamilton had to sit out the last half hour after an oil pressure problem stopped him on track with 30 minutes remaining.
That meant the 2008 champion, who is 29 points adrift of Rosberg after eight races, did only 14 laps after lunch compared to Rosberg's 35 and was unable to do an important long run race simulation.
The German ended the day second fastest and 0.228 off Hamilton's pace in the afternoon.
"It happens. I don't know why it happens to my car so much. I don't really know what the car feels like for the race but I will try to get some long runs tomorrow, said Hamilton, who has suffered two race retirements this season.
The Briton will be able to study Rosberg's data but he said that would not help much because of their different styles.
"It's OK, I'll be all right," he added.
WOMAN DRIVER
Rosberg was quickest in a morning session notable for the presence of a woman driver, Susie Wolff, for the first time in 22 years.
Hamilton is determined to regain the championship momentum after being beaten by his team mate in the last three grands prix. The Briton has won four races to Rosberg's three so far.
Ferrari's Fernando Alonso was third on the timesheets in both sessions with Red Bull's Australian Daniel Ricciardo fourth.
Red Bull's four times champion Sebastian Vettel was fifth in the afternoon.
Wolff suffered considerably more frustration than Hamilton after her involvement in the opening session, at the wheel of the car to be raced by Finland's Valtteri Bottas on Sunday, lasted barely 20 minutes.
On a bad morning for Williams, who finished third and fourth in Austria the weekend before last, Brazilian Felipe Massa then brought out the red flags after a heavy crash that also ruled him out of the rest of the morning.
Wolff, wife of Mercedes motorsport head Toto, managed just four laps before an oil pressure problem forced her to park up by the side of the track on a sunny but breezy morning at Silverstone.
Even if that ended her track activities, Wolff was still the first woman to take part in any stage of a grand prix weekend since Italian Giovanna Amati tried and failed to qualify with Brabham in 1992.
Italian Lella Lombardi, in 1976, was the last woman to race in Formula One.
"It was a really tough day but that's Formula One sometimes. We had an oil pressure problem which cut the engine," she said.
"Once I had put the helmet on that was the best feeling, and as soon as I had left the pit lane, everything felt good. Unfortunately it was a short run but I'm going to look forward to Hockenheim," added the Scot, who will have a second run at the German Grand Prix later this month.
Massa spun and hit the wall hard near the exit to Stowe corner with just over an hour of practice remaining, bringing the session to a halt. The Brazilian was unhurt in the impact but the car suffered heavy damage.
"I'm fine. I hit the outside of the kerb and it just pushed me inside," said the former Ferrari driver, who will be starting his 200th race this weekend but first at Silverstone with a British team.
(Reporting by Alan Baldwin, editing by Keith Weir/Rex Gowar)
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