Shah, who missed the opening test in Abu Dhabi due to an injury, was adjudged the player of the series for his 15 wickets in two matches.
"If you look back at the whole series, there was contribution from everyone. That's really pleasing for me as a team," Pakistan captain Misbah-ul-Haq, 41, said at the presentation, while adding he was still undecided on his international future.
England had resumed the day on 46-2 chasing 284 for a series-levelling win at the Sharjah Cricket Stadium but the tourists were reduced to 59-6 after the first seven overs of the morning.
Shah made the opening breakthrough by dismissing Joe Root (six) leg before wicket in the second over of the day and then trapped Jonny Bairstow (zero) in front of the stumps as the batsman attempted a sweep shot.
Left-arm spinner Zulfiqar Babar provided able support by dismissing James Taylor (two) and Samit Patel for a duck as England lost four wickets for 13 runs in the morning.
Captain Alastair Cook did offer resistance, completing his 46th half century in tests, with a stand of 49 runs for the seventh wicket with Adil Rashid, who was out shortly before the lunch break.
Stuart Broad was then removed by Shah for 20 with Cook (63) following shortly after to Malik, who was playing in his final test before retirement.
Ben Stokes (12) came out to bat despite a broken collarbone before being the last man out.
Cook said his team's failure to win the key moments in the game proved crucial.
"It's a hard place to come and play. We competed really well in all three of the games but at critical moments we couldn't dominate Pakistan," Cook said.
"It's always a learning curve but unfortunately international cricket isn't just about learning. It's about getting results."
The teams will next play four one-day internationals and three Twenty20 matches.
(Writing by Sudipto Ganguly in Mumbai; editing by Patrick Johnston)
