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Tom O’Connor scored a late goal for the Gills as they left Bristol Rovers with a point.
Gillingham lost experienced man Barry Fuller to injury and were a goal down at the break through Tyler Smith’s effort.
The Gills tried several different formations in the match and finally got their reward when O’Connor struck seven minutes from time.
Rovers started the night two places and two points above the Gills, hoping to preserve their unbeaten start to the league season at home. Steve Evans’ side were looking for their first away win.
There were two changes for the Gills, both in attack, with Alex Jakubiak returning to the XI to face his former club and weekend game-changer Brandon Hanlan also back in from the start.
Hanlan went close to converting at the near post, after Max Ehmer flicked on Mark Byrne's throw, but clear-cut chances were hard to come by during the half.
There was an early injury blow for the Gills when Fuller limped out of the action after only 13 minutes and was replaced at right-back by youngster Jack Tucker. It was only a second league appearance for the 19-year-old, his last coming two years before.
Olly Lee fired a half chance over for the Gills and Connor Ogilvie headed a chance wide of the mark from a corner.
Rovers forward Jonson Clarke-Harris went close on a couple of occasions. One looping header beat keeper Jack Bonham but not O'Connor on the line and moments later he headed a cross wide of the post.
The hosts took the lead on 39 minutes. A ball from the left flank was fed into Smith, he ran at a retreating Gills defence, jinking one way and then the other, before firing in a low shot.
There were more injury concerns before the break, with physio Gary Hemens on to treat Bonham after he landed awkwardly. He also attended to the keeper after the referee blew his whistle for half-time.
The Gills had shown some better glimpses in and around the box just before the break but Ndjoli was replaced by Mark Marshall as the Gills switched to a two-man front-line of Jakubiak and Hanlan, having started 4-2-3-1.
Rovers had a couple of early second half efforts that Bonham watched go wide of his goal. Alfie Kilgour tried his luck from long-distance and Liam Sercombe smashed a shot over after Josh Hare’s cross found its way into his path.
Home sub Sercombe had another shot blocked as the Gills continued to be on the backfoot. Ed Upson grazed the outside of the post with his shot on the hour mark.
The Gills - who switched again to wing-backs - had a chance from a set-piece, taken by Lee, but keeper Anissi Jaakkola held on with the ball heading into the top corner.
Rovers lost Hare to injury with 15 minutes left, the former Gills player being stretchered off the field.
The Gills levelled on 83 minutes. Lee’s cross was met by Ogilvie, unmarked at the far post, and when his shot was saved, O’Connor was well placed to turn the ball home.
O’Connor had another chance late on as Rovers failed to pick him up. Jaakkola made the save and the loose ball was cleared.
A deflected shot from Byrne nearly won it for Gills, at the end of the six added-on minutes.
Bristol Rovers: Jaakkola, Ogogo, Craig, Upson, Clarke (Sercombe 54mins), Clarke-Harris, Leahy, Kilgour, Davies, Smith (Adeboyejo 80mins), Hare (Little 74mins). Subs not used: Van Stappershoef, Nichols, Bennett, Rodman.
Gillingham: Bonham, Fuller (Tucker 13mins), O’Connor, Ehmer, Ogilvie, Jones, Byrne, Lee, Jakubiak, Ndjoli (Marshall 46mins), Hanlan (Mandron 62mins). Subs not used: Walsh, O'Keefe, Pringle, Charles-Cook.
Attendance: 6,370 (231 Gills fans)