Alvaro Negredo put the visitors ahead deep into first-half stoppage time before Scott Dann equalised ten minutes into the second period.
City were below par all afternoon and were lucky not to suffer a shock cup exit as Boyata was given his marching orders for two silly fouls.
Manuel Pellegrini made seven changes to the side that beat Swansea on New Year’s day, though the quality and strength in depth at his disposal meant that they were able to field a strong side.
It was the hosts that provided much of the attacking intent throughout the opening half, however. Costel Pantilimon had to be on his toes a number of times to race off his line and clear the danger ahead of the chasing Rudy Gestede.
City began to find their feet as the half wore on, though, and had Blackburn – who had pressed high and in numbers – penned in their own half for the final 10 minutes of the opening period.
It looked as if the two sides would go into the break on level terms until an unmarked Negredo latched onto Edin Dzeko’s knock-down at the far post, turning the ball past a helpless Paul Robinson.
The home side started the second half in a similarly positive manner to which they started the first, and were justly level after ten minutes.
Tom Cairney’s floated corner was met by the towering Gestede, whose header could only be flapped at by Pantilimon. Dann was the quickest to react, poking the ball into an empty net from four yards.
Bowyer introduced Jordan Rhodes and DJ Campbell late on, and though Boyata was shown a second yellow for a silly foul on the latter, the hosts were unable to convert their numerical advantage into a vital win.
20’ – FIRST CHANCE: Marshall’s corner is floated in from the left towards the far post. Centre-half Dann rises highest and powers a header at goal from 10 yards. It's straight at Pantilimon, though, and the keeper is able to make a comfortable save.
30’ – HALF-CHANCE: Lovely bit of skill from Negredo who receives a sharp pass and flicks the ball over the top of Hanley to put himself through on goal. Robinson is off his line in a flash to gather at his feet. Great bit of improvisation.
35’ – CITY TURNING THE SCREW: This is a real period of sustained pressure from City. Boyata overlaps down the right and pulls the ball back to Silva who is unmarked 10 yards from goal. The Spaniard leans back and sends the ball high over the bar. A warning for Blackburn.
45’ – GOAL: Silva's corner from the left is met by Dzeko 12 yards from goal. The striker's header is wayward but Negredo is on hand at the far post to prod home from four yards. Hint of offside. Simple finish. Shoddy defending.
55’ – GOAL: Blackburn are level. Cairney’s corner is met by the towering Gestede. Pantilimon can’t hold the ball and it rolls to Dann five yards from goal. The captain duly sidefoots the ball into the back of the net.
64’ – GOLDEN CHANCE MISSED: Dzeko has a pop at goal from 20 yards that Robinson can only palm into the path of Negredo. With the keeper lying on the floor, all he has to do is nod it home - but he diverts his header wide of the target.
78’ – GREAT SAVE: Top stop from Robinson. Navas picks the ball up 30 yards from goal and travels forward before sending a dipping effort towards the far post. Robinson is down well to beat the ball around the post.
83’ – CHANCE TO NICK IT: The two substitutes – Rhodes and Campbell – combine straight away. Rhodes skips down the right and hangs the ball up for Campbell, who heads marginally wide from 12 yards.
85’ - RED CARD: Boyata is sent off. Stupid, stupid second yellow. The young full-back has a swipe at Campbell and is lucky not to be shown a straight red.
87’ - SO CLOSE: Cairney receives the ball on the right and wriggles away from Clichy to have a shot at goal. Pantilimon looks worried but is fortunate to see it fly wide of his far post.
Paul Robinson made his first appearance in over a year after surgery to remove a blood clot on the lung.
The teams have now met seven times in the FA Cup, with Blackburn unbeaten in the last two - following a 2-0 win at Ewood Park in 2007.
TALKING POINT - Have Blackburn blown their chance to progress into the fourth round?
At 1-1, at home and with a numerical advantage, Blackburn surely missed out on a glorious chance to spring a huge shock in the FA Cup. They now face a daunting task of going to the Etihad Stadium where City have a 100% record in the Premier League this season.
MAN OF THE MATCH
Scott Dann, Blackburn - The Blackburn skipper was a rock at the heart of the Rovers defence all day. Composed with the ball at his feet and a threat in the air, City struggled to cope with him offensively or defensively. His goal capped an excellent perfomance.
BLACKBURN: Robinson 6, Henley 6, Dann 8, Hanley 7, Spurr 6, Cairney 6, Lowe 6, Taylor 6, Williamson 6, Marshall 7, Gestede 7
SUBS: King 6, Campbell 5, Rhodes 6
MAN CITY: Pantilimon 6, Boyata 4, Lescott 7, Nastasic 6, Clichy 6, Milner 7, Fernandinho 6, Javi Garcia 6, Silva 7, Negredo 7, Dzeko 6
SUBS: Zabaleta n/a, Jesus Navas 6, Toure 6