England, having lost the toss in overcast seam bowler-friendly conditions, closed on their tea score of 127 for two after rain washed out the day's final session in what was the 2,000th Test in history.
Trott, missed twice, was 58 not out and Kevin Pietersen 22 not out with the two South Africa-born batsmen's unbroken third wicket stand so far worth 65 in what was also the 100th Test between England and India.
Left-arm fast bowler Zaheer had been the pick of India's attack, with two wickets for 18 runs in 13.3 overs, when he suffered what appeared to be a hamstring injury and slowly walked off the field with England 107 for two.
There was a bizarre conclusion to the day with players and spectators hanging around until 6:30pm local time in the hope of a resumption under the Lord's floodlights.
But some two hours and 20 minutes after bad light forced an early tea, fresh drizzle prompted the umpires to finally call play off for the day.
Earlier, after Zaheer went off, the unflustered Trott drove off-spinner Harbhajan Singh for four.
But he was lucky to be at the crease at all by that stage.
Before lunch he'd been missed on eight when, to Harbhajan's first ball of the match, he got an outside edge that slip Rahul Dravid could not grasp.
And Trott should have been out for 32 in the second session when, having nicked Zaheer, he saw India captain and wicketkeeper Mahendra Singh Dhoni inexplicably fail to move across to his right for a catch that was never going to carry to first slip Dravid.
Trott went on to complete a valuable 89-ball fifty with seven boundaries.
ICC Test Championship leaders India had held England to 43 for one off 21 overs at lunch in an old-fashioned, attritional opening session after rain had delayed the start by 30 minutes.
Zaheer had in-form opener Alastair Cook lbw for just 12, the first time in seven Test innings the left-hander had failed to make a fifty.
Shortly after lunch, India did reduce England to 62 for two when captain Andrew Strauss, on his Middlesex home ground, miscued a pull off a Zaheer bouncer straight to Ishant Sharma at long leg and was out for 22.
It was a welcome sight for India after Strauss had made 78 and 109 not out 'guesting' for Somerset in their lone, drawn, warm-up match last week.
Although seamers Praveen Kumar and Sharma bowled tidily, neither had the wicket-taking threat of Zaheer.
If England win this four-match series by two Tests they will displace India at the top of the Test standings.
England 1st Innings
- A. Strauss c Sharma b Zaheer Khan 22
- A. Cook lbw b Zaheer Khan 12
- J. Trott not out 58
- K. Pietersen not out 22
- Extras (b8, lb4, w1) 13
- Total (2 wkts, 49.2 overs, 222 mins) 127
- To bat: I Bell, E Morgan, M Prior, S Broad, G Swann, C Tremlett, J Anderson
- Fall of wickets: 1-19 (Cook), 2-62 (Strauss)
- Bowling: Zaheer Khan 13.3-8-18-2; Kumar 17.3-5-46-0; Sharma 11.2-3-33-0 (1w); Harbhajan 7-1-18-0
- Toss: India
- Umpires: Billy Bowden (NZL) and Asad Rauf (PAK)
- TV umpire: Marais Erasmus (RSA)
- Match referee: Ranjan Madugalle (SRI)