In Q1 Hamilton was seen moving off the track through a wet Eau Rouge - Raidillon complex on driver's left and rejoined the track directly ahead of team-mate George Russell, when both Mercedes drivers were on their out laps.
Russell had to take avoiding action, while behind them the Alfa Romeo of Valtteri Bottas was also hindered.
The incident was reported to the stewards, who investigated it after the qualifying session when both Hamilton and Russell were summoned.
Hamilton argued he simply wanted to jump out of the way of Bottas, who had just started a flying lap.
Russell also explained he wanted to make sure Bottas wasn't impeded, and thought there was no danger to the way Hamilton rejoined the racing surface atop Raidillion.
The stewards followed their reasoning and decided to take no further action.
"Hamilton explained that he had been warned of the approach of Bottas and moved out of the way, in this case off track," they wrote in their verdict.
"Russell explained that he had the same warning but moved out of the way later.
"He also explained that as he was on the same program as Hamilton he was fully aware of what Hamilton was doing and that at no point was the manoeuvre unsafe. The Stewards agree and take no further action."
Williams driver Alex Albon was also investigated for an unsafe rejoin. Albon went off the road in Q1 in the second sector and then rejoined on the racing line right in front of the Alpine of Pierre Gasly.
Albon was given a reprimand for the offence, with the stewards conceding that Albon was automatically going to end up on the ideal line when he returned to the track but also noting he could have taken more care.
"Albon left the circuit at Turn 8 at the end of Q1. He then rejoined the circuit on the racing line.
"While he was always going to have to rejoin on the line, the Stewards feel that he could have done more to ensure that he rejoined safely while another car was approaching."
Haas driver Kevin Magnussen received a three-place grid drop for impeding Ferrari's Charles Leclerc.
Magnussen hit the wall coming out of Speaker's Corner and then remained on the racing line for the following corners, significantly impeding Leclerc, who furiously called for a penalty on the team radio.
