Ipswich stretched their unbeaten run to four matches and hit the 50-point mark while FA Cup semi-finalists Millwall remain a point better off.
Andy Keogh had a goal disallowed and clipped the woodwork for the hosts while David Forde denied Luke Hyam in the first half.
The Lions had the ball in the net after five minutes but Keogh had just strayed offside as he converted Jermaine Easter's cross.
Town keeper Scott Loach had a nervy moment when he fumbled a cross from Richard Chaplow but he was able to recover before John Marquis could pounce while Keogh's lob bounced off the top of the bar.
Millwall had dominated the first half but were almost caught out as the interval approached.
First, a poor clearance from Forde fell to Luke Hyam, who tried his luck with a 50-yard lob but the ball held up in the wind and Mark Beevers got back in time to spare his keeper's blushes.
And moments later Forde redeemed himself with a stunning save from Hyam.
Nouble's cross was met with a fierce, first-time volley from the midfielder but Forde got a firm hand to the ball down low and Alan Dunne was able to complete the clearance.
After the break, Lions sub Rob Hulse almost broke the deadlock but did not get a clean connection as he steered the ball goalwards and Loach was able to block.
Then Lowry's wind-assisted corner caused mild panic in the Ipswich area but the goalmouth scramble ended with Trotter blazing over.
Nouble should have done better after Emmanuel-Thomas' shot was parried by Forde but the former West Ham striker fired too high.
Millwall looked the likelier to score towards the end, but Lowry rattled the post with a curling free-kick and Easter fired a late chance wide as they had to settle for a point.