Ipswich largely controlled the first half at Portman Road, but went in at the interval a goal down following Joel Grant's stunning strike in the 42nd minute.
Town were booed off by a section of the home crowd at the break, but the Tractor Boys responded and goals from Daryl Murphy and Aaron Cresswell secured the three points to lift Ipswich into the top half of the Sky Bet Championship.
Johnson said: "I needed to go through a few things with the boys. We lacked the energy and competitiveness in the second half - we have to play the game more vigorously.
"We gave Ipswich time and room and you can't do that at this level. You have to be more clever.
"We did enough in the first half to be 1-0 up, but we were a little disorganised after the restart.
"We allowed Ipswich's experienced strikers to hold the ball up and their experienced full-backs to get forward. We didn't do enough in the final third."
A surprise win, which would have been Yeovil's first since the opening day, looked on the cards at half-time after Grant had found the top corner from 20 yards - a strike described as "fantastic" by Johnson.