Alonso returned to the track with a little more than 30 minutes remaining of the second practice session, and managed to haul his McLaren up to seventh in the order, just 1.3 sec off Raikkonen's best time.
Teams will have the same three types of ultra-soft, super-soft and soft compound tyres that Mercedes, and Hamilton in particular, struggled with in Monaco and Russian Federation, the only other race this year the Briton has finished off the podium.
After the session, Vettel admitted it had hampered his learning during his long run but said his frustration was more with the situation than Hamilton himself. I spun twice today. "On the last lap I made a mistake in corner two and improved a little bit but just couldn't make the laps very good and paid the price for it".
When Mercedes switched to the ultra-softs in the second-half of the session, Bottas and Hamilton traded fastest times.
This weekend will also see Fernando Alonso return to Formula One after an impressive if not ultimately successful outing in the Indy 500. Hamilton and Bottas needed the second lap to warm their tyres up, but on his second lap, Hamilton shot to the top and dropped Pascal Wehrlein into the elimination zone. Stoffel Vandoorne (BEL/McLaren) 1:15.943 (29), 12.
During the first session, Alonso was told by his engineer to stop on track.
The failure came as McLaren executive director Zak Brown again said that Honda had to up their game if the partnership was to have a future. "Today we showed that we can have an answer (to Ferrari) if we put the work in".
"The drivers' championship is there job and they are free to do it until the numbers are going clearly in one direction or the other - in that case we would apply our rules of engagement".
"I am always the skeptic when it comes to making predictions - but that's the mind-set we need to cover all the bases tonight and have a strong race". Maybe take some risks, do things they wouldn't normally do.
"You never know here, it's one of those places things can change quite quickly".
Asked if they had been discussing a customer engine supply with Mercedes, Brown said: "We have a plan B, a Plan C. We have some plans".
Vettel was the first auto out on track for Q3, but on his first timed lap he locked up going into the hairpin and compromised his run down the straight.
Max Verstappen finished fifth for Red Bull, but it was far from a straightforward day for the Milton Keynes team after the Dutchman parked his auto following a gearbox failure, while engine problems restricted Daniel Riccciardo's running in the sister vehicle.