The Shrimps’ winger celebrated his 40th birthday on Saturday and was substituted to a standing ovation deep into the second half.
For good measure, he was also named as Morecambe’s man of the match against one of his former clubs.
“I know we’ve had six points from the last two (games) but it’s put a dampener on it,” Ellison said after collecting his man of the match award.
“They (Lincoln) are big, strong and organised but Bury are the best footballing team that have come here.
“They are top of the table and they are effective at what they do, so fair play to them.”
The Shrimps had gone into the game after wins at Port Vale and Oldham Athletic.
However, they were a clear second best against the League Two leaders for whom Bruno Andrade netted twice.
With chances at a huge premium for Morecambe, the closest they came was on 81 minutes when Lincoln keeper Matt Gilks denied Ritchie Sutton with some of the home fans thinking the ball had actually crossed the line.
“I think it was a good save,” Ellison said.
“It was on the line, and if that had gone in, the game may have been edgy for the last 10 or 15 minutes.
“For whatever reason, we didn’t get started in the first half but if you had said we’d take six points from nine, we’d have snapped your hand off.”
The defeat meant Morecambe stayed 20th in League Two with a dozen games of the season still to be played.
Of the teams below them, bottom side Notts County lost at Tranmere Rovers to remain seven points behind the Shrimps.
Second-bottom Macclesfield Town closed to within five points after a draw at Crawley Town, third-bottom Port Vale lost at Cheltenham Town, while Yeovil Town earned three points against Cambridge United.
Yeovil are next up for the Shrimps, who travel to Huish Park on Saturday.
“It’s another massive game,” Ellison acknowledged.
“We’re going down there and we need to put in a performance and get the win.”