In testing humid conditions at Gresty Road Rovers were given a good workout by a lively Crewe side, but it was the former Railwayman youngster Hanley who scored the only goal of the game on 11 minutes.
Mathias Pogba and Ryan Colclough went close for the home side, whist Ruben Rochina and Alan Judge both had opportunities to stretch the visitor's lead.
The second half saw Bowyer give senior experience to some of his former youth team players and they performed admirably in the final 20 minutes to ensure Rovers claimed the win.
Earlier in the day a Rovers XI defeated Fleetwood 4-1 in a behind closed doors game at Brockhall, DJ Campbell (2), Leon Best and Josh King the goalscorers.
Despite this Gary Bowyer was still able to name a strong starting eleven for the evening game at Gresty Road. In front of Jake Kean were a back four of Todd Kane, Grant Hanley, Scott Dann and Markus Olsson, Alex Marrow got his first minutes under his belt on home soil along side Jason Lowe in midfield, whilst further forward Chris Taylor, Alan Judge and Ruben Rochina operated behind Jordan Rhodes up front.
The home side had threatened early on through Mathias Pogba but it was Rovers who took the lead when Ruben Rochina's corner was powerfully headed home by Scottish international Hanley.
Crewe, as expected, were neat and tidy in possession, Ryan Colclough catching the eye when he skipped past Markus Olsson and Hanley but he put his near post shot wide of goal.
Byron Moore tested Jake Kean with a shot from distance and from the resulting corner Colclough again fired narrowly wide.
As the half wore on Rovers started to gain more control, Alan Judge going close on two occasions with shots across the area.
Lovely play by substitute Fabio Nunes saw him tee up Ruben Rochina who struck the ball sweetly on the volley but it hit the back of Jordan Rhodes and bounced behind.
Rochina would test Crewe once more in the final minutes of the opening period, stinging the gloves of Steve Phillips with a low drive.
At the start of the second half a neat pass from Alan Judge teed up Chris Taylor on the edge of the box but his steered effort was saved by substitute Alan Martin. Then Jordan Rhodes tried his luck from distance with a shot on the turn, he shot lacking accuracy.
As the match wore on substitutions were the order of the day, and one of the Crewe newcomers, Oliver Turton, went close to equalising but steered the ball over.
Mathias Pogba had been a threat for spells in the game, on 68 mines the striker powered a diving header just over the bar as the home side went looking to get back on level terms.
Crewe are renowned for their young players coming through, and Gary Bowyer also gave some of his former youth team charges some game time, playing the last twenty minutes and performing well against a well organised Crewe outfit.
The final chance fell to Crewe, but goalkeeper Matty Urwin ensured that it would be Rovers claiming the victory with a last-gasp close-range save. Saving well to thwart substitute Dominic Smith.
CREWE: Phillips (sub Martin 46 mins), Mellor, Tootle (sub Guthrie 65 mins), West (sub Turton 65 mins), Ray (sub Dugdale 65 mins), Audel (sub Ellis 65 mins), Colclough (sub Murdoch 75 mins), Osman (c) (sub Jones 87 mins), Pogba (sub Nolan 87 mins), Clayton (sub Smith 87 mins), Moore (sub Waters 70 mins).
Attendance: 1922 (243 Rovers fans).