Adebayo Akinfenwa opened the scoring four minutes in as Gillingham hoped to extend Orient's winless league run to five matches.
Marvin Bartley equalised with 20 minutes left and Yohann Lasimant then struck in the 90th minute to ensure Orient continue to lead the way.
Wolves kept pace with Orient at the top of the table thanks to a 2-0 home win over Crewe Alexandra.
Michael Jacobs got Wolves off to the perfect start by finding the net in the third minute as Crewe looked to be in for a long day.
Wolves, however, failed to really make sure of the win until the 92nd minute as Scotland international Leigh Griffiths completed the scoring, moving his side on to 47 points.
A 3-2 win over visitors Swindon Town gave Brentford a fifth consecutive league win and extending their unbeaten run in the division to 11 matches.
Goals by Ryan Mason and Nicky Ajose either side of a Sam Saunders effort gave Swindon a 2-1 lead by the 53rd minute, but Clayton Donaldson equalised for Brentford just a few moments later.
Marcello Trotta then netted Brentford's winner 19 minutes from the end to bring them one point behind the top two.
Preston North End strengthened their position in the play-off places thanks to a 1-0 victory at Carlisle United, but Peterborough United were unable to follow suit as mid-table Coventry City beat them 4-2.
A fourth win from five league matches was the reward for sixth-placed Rotherham United as they defeated hosts Bradford City 1-0, while Colchester United picked up the result of the day by hammering Stevenage 4-0.
Towards the bottom of the table, Sheffield United and fellow strugglers Oldham Athletic drew 1-1 at Bramall Lane, while Tranmere Rovers' 1-0 victory at Shrewsbury Town moved them four points clear of the drop zone.
A 1-0 home win over Walsall was not enough to catapult Bristol City out of the bottom four, Notts County stay in 23rd after losing 2-1 at Port Vale and MK Dons moved into the top half thanks to 2-0 triumph over hosts Crawley Town.
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